4-137832570-T-C

Variant names:

• chr4-137832570-T-C
• rs1509269

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.894 in 152,200 control chromosomes in the GnomAD database, including 60,840 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 0.89 (60840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.893 AC: 135882 AN: 152082 Hom.: 60787 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.914

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.894 AC: 135994 AN: 152200 Hom.: 60840 Cov.: 32 AF XY: 0.893 AC XY: 66416 AN XY: 74410

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.913

Alfa AF: 0.896 Hom.: 19858

Bravo AF: 0.899

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1509269; hg19: chr4-138753724;