rs4657493

chr1-165947872-G-T

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 0.234 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.243

Alfa AF: 0.226 Hom.: 8103

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4657493; hg19: chr1-165917109;