rs1472955

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_079420.3(MYL1):​c.133-1399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,856 control chromosomes in the GnomAD database, including 12,290 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.40 ( 12290 hom., cov: 31)

Consequence

MYL1
NM_079420.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.268
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYL1NM_079420.3 linkuse as main transcriptc.133-1399T>C intron_variant ENST00000352451.4 NP_524144.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYL1ENST00000352451.4 linkuse as main transcriptc.133-1399T>C intron_variant 1 NM_079420.3 ENSP00000307280 P05976-1

Frequencies

GnomAD3 genomes
AF:
0.400
AC:
60769
AN:
151738
Hom.:
12252
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.372
Gnomad AMI
AF:
0.524
Gnomad AMR
AF:
0.498
Gnomad ASJ
AF:
0.439
Gnomad EAS
AF:
0.450
Gnomad SAS
AF:
0.458
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.490
Gnomad NFE
AF:
0.375
Gnomad OTH
AF:
0.414
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
60869
AN:
151856
Hom.:
12290
Cov.:
31
AF XY:
0.409
AC XY:
30396
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.372
Gnomad4 AMR
AF:
0.499
Gnomad4 ASJ
AF:
0.439
Gnomad4 EAS
AF:
0.450
Gnomad4 SAS
AF:
0.460
Gnomad4 FIN
AF:
0.460
Gnomad4 NFE
AF:
0.375
Gnomad4 OTH
AF:
0.415
Alfa
AF:
0.399
Hom.:
1940
Bravo
AF:
0.400
Asia WGS
AF:
0.496
AC:
1722
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
3.5
DANN
Benign
0.40

Splicing

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: rs1472955; hg19: chr2-211168638; API