Variant chr2-210302408-A-T 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.160+80T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,347,298 control chromosomes in the GnomAD database, including 102,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 12604 hom., cov: 32)

Exomes 𝑓: 0.38 ( 89600 hom. )

Consequence

MYL1
NM_079420.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.452

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 2-210302408-A-T is Benign according to our data. Variant chr2-210302408-A-T is described in ClinVar as [Benign]. Clinvar id is 1294855.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.491 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.160+80T>A		intron_variant		ENST00000352451.4
MYL1	NM_079422.3 linkuse as main transcript	c.28+360T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
MYL1	ENST00000352451.4 linkuse as main transcript	c.160+80T>A	intron_variant	1	NM_079420.3		P05976-1
MYL1	ENST00000341685.8 linkuse as main transcript	c.28+360T>A	intron_variant	1		P1	P05976-2
MYL1	ENST00000484290.1 linkuse as main transcript	n.291+80T>A	intron_variant, non_coding_transcript_variant	5
MYL1	ENST00000496436.5 linkuse as main transcript	n.263+360T>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.406

AC:

61577

AN:

151802

Hom.:

12563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.522

Gnomad AMR

AF:

0.500

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.459

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.417

GnomAD4 exome

AF:

0.383

AC:

458084

AN:

1195378

Hom.:

89600

AF XY:

0.385

AC XY:

229880

AN XY:

597512

show subpopulations

Gnomad4 AFR exome

AF:

0.391

Gnomad4 AMR exome

AF:

0.551

Gnomad4 ASJ exome

AF:

0.431

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.456

Gnomad4 FIN exome

AF:

0.448

Gnomad4 NFE exome

AF:

0.364

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.406

AC:

61681

AN:

151920

Hom.:

12604

Cov.:

AF XY:

0.415

AC XY:

30794

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.391

Gnomad4 AMR

AF:

0.501

Gnomad4 ASJ

AF:

0.438

Gnomad4 EAS

AF:

0.452

Gnomad4 SAS

AF:

0.460

Gnomad4 FIN

AF:

0.459

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.418

Alfa

AF:

0.390

Hom.:

1465

Bravo

AF:

0.406

Asia WGS

AF:

0.498

AC:

1728

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

0.73

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