Variant 2-210294131-T-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 NM_079420.3(MYL1):c.478+114A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,130,324 control chromosomes in the GnomAD database, including 7,286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1421 hom., cov: 32)

Exomes 𝑓: 0.10 ( 5865 hom. )

Consequence

MYL1
NM_079420.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.572

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=-0.84).

BP6

Variant 2-210294131-T-C is Benign according to our data. Variant chr2-210294131-T-C is described in ClinVar as [Benign]. Clinvar id is 1227782.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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.478+114A>G		intron_variant		ENST00000352451.4
MYL1	NM_079422.3 linkuse as main transcript	c.346+114A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4 linkuse as main transcript	c.478+114A>G	intron_variant	1	NM_079420.3		P05976-1
MYL1	ENST00000341685.8 linkuse as main transcript	c.346+114A>G	intron_variant	1		P1	P05976-2
MYL1	ENST00000484290.1 linkuse as main transcript	n.609+114A>G	intron_variant, non_coding_transcript_variant	5
MYL1	ENST00000496436.5 linkuse as main transcript	n.581+114A>G	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.123

AC:

18697

AN:

152138

Hom.:

1400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.0854

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.00557

Gnomad SAS

AF:

0.133

Gnomad FIN

AF:

0.0442

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0992

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.101

AC:

98631

AN:

978068

Hom.:

5865

AF XY:

0.102

AC XY:

49119

AN XY:

482848

show subpopulations

Gnomad4 AFR exome

AF:

0.211

Gnomad4 AMR exome

AF:

0.0801

Gnomad4 ASJ exome

AF:

0.137

Gnomad4 EAS exome

AF:

0.00261

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.0447

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.111

GnomAD4 genome

AF:

0.123

AC:

18757

AN:

152256

Hom.:

1421

Cov.:

AF XY:

0.120

AC XY:

8945

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.0853

Gnomad4 ASJ

AF:

0.157

Gnomad4 EAS

AF:

0.00559

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.0442

Gnomad4 NFE

AF:

0.0992

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.112

Hom.:

148

Bravo

AF:

0.130

Asia WGS

AF:

0.0740

AC:

259

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

-0.84

CADD

Benign

2.2

DANN

Benign

0.56

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