rs4657493

Variant names:

• chr1-165947872-G-T
• rs4657493

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 0.234 in 152,164 control chromosomes in the GnomAD database, including 4,318 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 0.23 (4318 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 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: 0.234 AC: 35554 AN: 152046 Hom.: 4314 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.234 AC: 35576 AN: 152164 Hom.: 4318 Cov.: 33 AF XY: 0.236 AC XY: 17530 AN XY: 74388

African (AFR) AF: 0.237 AC: 9823 AN: 41514

American (AMR) AF: 0.238 AC: 3644 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3468

East Asian (EAS) AF: 0.147 AC: 760 AN: 5182

South Asian (SAS) AF: 0.354 AC: 1705 AN: 4816

European-Finnish (FIN) AF: 0.255 AC: 2705 AN: 10590

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15536 AN: 67990

Other (OTH) AF: 0.243 AC: 514 AN: 2116

Alfa AF: 0.227 Hom.: 16709

Bravo AF: 0.231

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.80
DANN	Benign	0.31
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4657493; hg19: chr1-165917109;