rs4660456

Variant names:

• chr1-40773839-A-G
• rs4660456

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.218 in 152,214 control chromosomes in the GnomAD database, including 4,278 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 0.22 (4278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.218 AC: 33130 AN: 152096 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.218 AC: 33151 AN: 152214 Hom.: 4278 Cov.: 32 AF XY: 0.224 AC XY: 16651 AN XY: 74428

African (AFR) AF: 0.100 AC: 4174 AN: 41542

American (AMR) AF: 0.338 AC: 5174 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2157 AN: 5168

South Asian (SAS) AF: 0.418 AC: 2019 AN: 4826

European-Finnish (FIN) AF: 0.225 AC: 2381 AN: 10598

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15434 AN: 67992

Other (OTH) AF: 0.246 AC: 519 AN: 2114

Alfa AF: 0.225 Hom.: 8508

Bravo AF: 0.216

Asia WGS AF: 0.425 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs4660456; hg19: chr1-41239511; COSMIC: COSV58129718;