chr3-123722120-G-A

Variant names:

• chr3-123722120-G-A
• rs820355
• NM_053025.4:c.1804+8C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_053025.4(MYLK):​c.1804+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.984 in 1,562,844 control chromosomes in the GnomAD database, including 759,676 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.92 (65766 hom., cov: 35)
  • Exomes 𝑓: 0.99 (693910 hom.)
• Consequence: MYLK NM_053025.4 splice_region, intron
• Scores: Splicing: ADA: 0.0002309
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:12
• Conservation: PhyloP100: 1.16
• Publications: 8 publications found

Genes affected

MYLK (HGNC:7590): (myosin light chain kinase) This gene, a muscle member of the immunoglobulin gene superfamily, encodes myosin light chain kinase which is a calcium/calmodulin dependent enzyme. This kinase phosphorylates myosin regulatory light chains to facilitate myosin interaction with actin filaments to produce contractile activity. This gene encodes both smooth muscle and nonmuscle isoforms. In addition, using a separate promoter in an intron in the 3' region, it encodes telokin, a small protein identical in sequence to the C-terminus of myosin light chain kinase, that is independently expressed in smooth muscle and functions to stabilize unphosphorylated myosin filaments. A pseudogene is located on the p arm of chromosome 3. Four transcript variants that produce four isoforms of the calcium/calmodulin dependent enzyme have been identified as well as two transcripts that produce two isoforms of telokin. Additional variants have been identified but lack full length transcripts. [provided by RefSeq, Jul 2008]

MYLK Gene-Disease associations (from GenCC):

• aortic aneurysm, familial thoracic 7

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• megacystis-microcolon-intestinal hypoperistalsis syndrome 1

  Inheritance: AR Classification: STRONG Submitted by: G2P
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: Unknown, AD Classification: STRONG, SUPPORTIVE Submitted by: ClinGen, Orphanet
• connective tissue disorder

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• megacystis-microcolon-intestinal hypoperistalsis syndrome

  Inheritance: AD, AR Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 3-123722120-G-A is Benign according to our data. Variant chr3-123722120-G-A is described in ClinVar as Benign. ClinVar VariationId is 226757.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_053025.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYLK	NM_053025.4	MANE Select	c.1804+8C>T		splice_region intron	N/A	NP_444253.3
	MYLK	NM_053027.4		c.1804+8C>T		splice_region intron	N/A	NP_444255.3
	MYLK	NM_053026.4		c.1597+8C>T		splice_region intron	N/A	NP_444254.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYLK	ENST00000360304.8	TSL:5 MANE Select	c.1804+8C>T		splice_region intron	N/A	ENSP00000353452.3	Q15746-1
	MYLK	ENST00000464489.5	TSL:1	n.*1383+8C>T		splice_region intron	N/A	ENSP00000417798.1	F8WBL7
	MYLK	ENST00000687848.1		c.1834+8C>T		splice_region intron	N/A	ENSP00000508761.1	A0A8I5KU53

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140396 AN: 152180 Hom.: 65739 Cov.: 35

Gnomad AFR AF: 0.735

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.937

GnomAD2 exomes AF: 0.980 AC: 167813 AN: 171256 AF XY: 0.984

Gnomad AFR exome AF: 0.734

Gnomad AMR exome AF: 0.986

Gnomad ASJ exome AF: 0.991

Gnomad EAS exome AF: 1.00

Gnomad FIN exome AF: 1.00

Gnomad NFE exome AF: 0.999

Gnomad OTH exome AF: 0.987

GnomAD4 exome AF: 0.991 AC: 1397833 AN: 1410546 Hom.: 693910 Cov.: 61 AF XY: 0.992 AC XY: 691147 AN XY: 696910

African (AFR) AF: 0.725 AC: 23318 AN: 32146

American (AMR) AF: 0.984 AC: 36936 AN: 37540

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 25022 AN: 25258

East Asian (EAS) AF: 1.00 AC: 36687 AN: 36688

South Asian (SAS) AF: 0.990 AC: 79072 AN: 79834

European-Finnish (FIN) AF: 1.00 AC: 49344 AN: 49364

Middle Eastern (MID) AF: 0.981 AC: 5612 AN: 5718

European-Non Finnish (NFE) AF: 0.999 AC: 1084551 AN: 1085496

Other (OTH) AF: 0.979 AC: 57291 AN: 58502

GnomAD4 genome AF: 0.922 AC: 140478 AN: 152298 Hom.: 65766 Cov.: 35 AF XY: 0.925 AC XY: 68862 AN XY: 74470

African (AFR) AF: 0.735 AC: 30534 AN: 41520

American (AMR) AF: 0.967 AC: 14801 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 3439 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5179 AN: 5180

South Asian (SAS) AF: 0.991 AC: 4783 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10627 AN: 10630

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67932 AN: 68036

Other (OTH) AF: 0.938 AC: 1984 AN: 2116

Alfa AF: 0.959 Hom.: 30476

Bravo AF: 0.912

Asia WGS AF: 0.981 AC: 3410 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	5	not specified (5)
-	-	4	Aortic aneurysm, familial thoracic 7 (4)
-	-	2	not provided (2)
-	-	1	Megacystis, microcolon, hypoperistalsis syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.47
PhyloP100		1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00023
dbscSNV1_RF	Benign	0.056
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs820355; hg19: chr3-123440967;