rs4660472

Variant names:

• chr1-40843046-A-G
• rs4660472

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 0.0988 in 152,236 control chromosomes in the GnomAD database, including 1,074 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 0.099 (1074 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.0989 AC: 15047 AN: 152118 Hom.: 1073 Cov.: 32

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0998

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0988 AC: 15043 AN: 152236 Hom.: 1074 Cov.: 32 AF XY: 0.0999 AC XY: 7436 AN XY: 74426

African (AFR) AF: 0.0439 AC: 1824 AN: 41558

American (AMR) AF: 0.118 AC: 1812 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2035 AN: 5166

South Asian (SAS) AF: 0.121 AC: 582 AN: 4818

European-Finnish (FIN) AF: 0.108 AC: 1142 AN: 10606

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0998 AC: 6791 AN: 68016

Other (OTH) AF: 0.107 AC: 226 AN: 2110

Alfa AF: 0.104 Hom.: 848

Bravo AF: 0.101

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.55
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs4660472; hg19: chr1-41308718;