2-210302408-A-T

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

2

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]

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
MYL1NM_079420.3 linkuse as main transcriptc.160+80T>A intron_variant ENST00000352451.4
MYL1NM_079422.3 linkuse as main transcriptc.28+360T>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYL1ENST00000352451.4 linkuse as main transcriptc.160+80T>A intron_variant 1 NM_079420.3 P05976-1
MYL1ENST00000341685.8 linkuse as main transcriptc.28+360T>A intron_variant 1 P1P05976-2
MYL1ENST00000484290.1 linkuse as main transcriptn.291+80T>A intron_variant, non_coding_transcript_variant 5
MYL1ENST00000496436.5 linkuse as main transcriptn.263+360T>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.406
AC:
61577
AN:
151802
Hom.:
12563
Cov.:
32
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.:
32
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 13, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
14
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.

Other links and lift over

dbSNP: rs2292300; hg19: chr2-211167132; API