Variant chr2-210303622-A-C 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 ENST00000341685.8(MYL1):c.-78T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,578,092 control chromosomes in the GnomAD database, including 189,139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 20857 hom., cov: 31)

Exomes 𝑓: 0.48 ( 168282 hom. )

Consequence

MYL1
ENST00000341685.8 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.69

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=-0.54).

BP6

Variant 2-210303622-A-C is Benign according to our data. Variant chr2-210303622-A-C is described in ClinVar as [Benign]. Clinvar id is 1239346.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 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.133-1107T>G		intron_variant		ENST00000352451.4
MYL1	NM_079422.3 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL1	ENST00000341685.8 linkuse as main transcript	c.-78T>G	5_prime_UTR_variant	1/7	1		P1	P05976-2
MYL1	ENST00000352451.4 linkuse as main transcript	c.133-1107T>G	intron_variant		1	NM_079420.3		P05976-1
MYL1	ENST00000484290.1 linkuse as main transcript		upstream_gene_variant		5
MYL1	ENST00000496436.5 linkuse as main transcript		upstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.522

AC:

79238

AN:

151872

Hom.:

20808

Cov.:

show subpopulations

Gnomad AFR

AF:

0.583

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.585

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.547

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.472

Gnomad OTH

AF:

0.528

GnomAD4 exome

AF:

0.483

AC:

688522

AN:

1426104

Hom.:

168282

Cov.:

AF XY:

0.485

AC XY:

343498

AN XY:

708948

show subpopulations

Gnomad4 AFR exome

AF:

0.590

Gnomad4 AMR exome

AF:

0.629

Gnomad4 ASJ exome

AF:

0.570

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.544

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.467

Gnomad4 OTH exome

AF:

0.506

GnomAD4 genome

AF:

0.522

AC:

79346

AN:

151988

Hom.:

20857

Cov.:

AF XY:

0.527

AC XY:

39119

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.584

Gnomad4 AMR

AF:

0.586

Gnomad4 ASJ

AF:

0.595

Gnomad4 EAS

AF:

0.452

Gnomad4 SAS

AF:

0.549

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.472

Gnomad4 OTH

AF:

0.527

Alfa

AF:

0.452

Hom.:

4111

Bravo

AF:

0.528

Asia WGS

AF:

0.541

AC:

1880

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 13, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.78

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