Variant chr2-210303478-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_079420.3(MYL1):c.133-963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 1,501,884 control chromosomes in the GnomAD database, including 7,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.078 ( 517 hom., cov: 32)

Exomes 𝑓: 0.094 ( 6756 hom. )

Consequence

MYL1
NM_079420.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.775

Variant links:

Genes affected

MYL1 (HGNC:7582): (myosin light chain 1) Myosin is a hexameric ATPase cellular motor protein. It is composed of two heavy chains, two nonphosphorylatable alkali light chains, and two phosphorylatable regulatory light chains. This gene encodes a myosin alkali light chain expressed in fast skeletal muscle. Two transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008]

MYL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 2-210303478-A-G is Benign according to our data. Variant chr2-210303478-A-G is described in ClinVar as [Benign]. Clinvar id is 1297941.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL1	NM_079420.3 linkuse as main transcript	c.133-963T>C		intron_variant		ENST00000352451.4
MYL1	NM_079422.3 linkuse as main transcript	c.3+64T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4 linkuse as main transcript	c.133-963T>C	intron_variant	1	NM_079420.3		P05976-1
MYL1	ENST00000341685.8 linkuse as main transcript	c.3+64T>C	intron_variant	1		P1	P05976-2
MYL1	ENST00000484290.1 linkuse as main transcript	n.74+64T>C	intron_variant, non_coding_transcript_variant	5
MYL1	ENST00000496436.5 linkuse as main transcript	n.74+64T>C	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0778

AC:

11837

AN:

152120

Hom.:

514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0602

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0691

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0842

Gnomad FIN

AF:

0.0435

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0976

Gnomad OTH

AF:

0.0789

GnomAD4 exome

AF:

0.0941

AC:

127060

AN:

1349646

Hom.:

6756

AF XY:

0.0945

AC XY:

63831

AN XY:

675156

show subpopulations

Gnomad4 AFR exome

AF:

0.0609

Gnomad4 AMR exome

AF:

0.0593

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.000318

Gnomad4 SAS exome

AF:

0.0813

Gnomad4 FIN exome

AF:

0.0439

Gnomad4 NFE exome

AF:

0.102

Gnomad4 OTH exome

AF:

0.0977

GnomAD4 genome

AF:

0.0778

AC:

11841

AN:

152238

Hom.:

517

Cov.:

AF XY:

0.0747

AC XY:

5560

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0602

Gnomad4 AMR

AF:

0.0691

Gnomad4 ASJ

AF:

0.157

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.0846

Gnomad4 FIN

AF:

0.0435

Gnomad4 NFE

AF:

0.0976

Gnomad4 OTH

AF:

0.0776

Alfa

AF:

0.0874

Hom.:

130

Bravo

AF:

0.0794

Asia WGS

AF:

0.0320

AC:

113

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.090

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over