Variant chr2-210303553-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The ENST00000341685.8(MYL1):c.-9C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00669 in 1,610,324 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0038 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 45 hom. )

Consequence

MYL1
ENST00000341685.8 5_prime_UTR

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.37

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 2-210303553-G-A is Benign according to our data. Variant chr2-210303553-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3037557.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYL1	NM_079420.3 linkuse as main transcript	c.133-1038C>T		intron_variant		ENST00000352451.4
MYL1	NM_079422.3 linkuse as main transcript	c.-9C>T		5_prime_UTR_variant	1/7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYL1	ENST00000341685.8 linkuse as main transcript	c.-9C>T	5_prime_UTR_variant	1/7	1		P1	P05976-2
MYL1	ENST00000352451.4 linkuse as main transcript	c.133-1038C>T	intron_variant		1	NM_079420.3		P05976-1
MYL1	ENST00000484290.1 linkuse as main transcript	n.63C>T	non_coding_transcript_exon_variant	1/6	5
MYL1	ENST00000496436.5 linkuse as main transcript	n.63C>T	non_coding_transcript_exon_variant	1/6	5

Frequencies

GnomAD3 genomes

AF:

0.00379

AC:

577

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000416

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00656

Gnomad OTH

AF:

0.000958

GnomAD3 exomes

AF:

0.00337

AC:

833

AN:

247314

Hom.:

AF XY:

0.00327

AC XY:

438

AN XY:

133878

show subpopulations

Gnomad AFR exome

AF:

0.000753

Gnomad AMR exome

AF:

0.00332

Gnomad ASJ exome

AF:

0.000499

Gnomad EAS exome

AF:

0.000111

Gnomad SAS exome

AF:

0.000694

Gnomad FIN exome

AF:

0.00209

Gnomad NFE exome

AF:

0.00542

Gnomad OTH exome

AF:

0.00501

GnomAD4 exome

AF:

0.00699

AC:

10193

AN:

1458118

Hom.:

Cov.:

AF XY:

0.00683

AC XY:

4951

AN XY:

725376

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00306

Gnomad4 ASJ exome

AF:

0.000614

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.000629

Gnomad4 FIN exome

AF:

0.00261

Gnomad4 NFE exome

AF:

0.00846

Gnomad4 OTH exome

AF:

0.00693

GnomAD4 genome

AF:

0.00379

AC:

577

AN:

152206

Hom.:

Cov.:

AF XY:

0.00360

AC XY:

268

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00321

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000416

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.00656

Gnomad4 OTH

AF:

0.000948

Alfa

AF:

0.00409

Hom.:

Bravo

AF:

0.00385

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MYL1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 03, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

9.8

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

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

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