rs1497957

Variant names:

• chr4-166189281-C-T
• rs1497957

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.427 in 151,796 control chromosomes in the GnomAD database, including 14,482 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 0.43 (14482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 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: 0.427 AC: 64786 AN: 151678 Hom.: 14465 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.427 AC: 64859 AN: 151796 Hom.: 14482 Cov.: 32 AF XY: 0.433 AC XY: 32125 AN XY: 74186

African (AFR) AF: 0.506 AC: 20949 AN: 41428

American (AMR) AF: 0.372 AC: 5667 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2197 AN: 5166

South Asian (SAS) AF: 0.598 AC: 2880 AN: 4820

European-Finnish (FIN) AF: 0.457 AC: 4802 AN: 10502

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25465 AN: 67860

Other (OTH) AF: 0.429 AC: 902 AN: 2102

Alfa AF: 0.396 Hom.: 16604

Bravo AF: 0.421

Asia WGS AF: 0.553 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1497957; hg19: chr4-167110433;