rs4667622

Variant names:

• chr2-170147675-G-A
• rs4667622

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 0.508 in 151,982 control chromosomes in the GnomAD database, including 20,849 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 0.51 (20849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 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: 0.508 AC: 77178 AN: 151864 Hom.: 20825 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.508 AC: 77242 AN: 151982 Hom.: 20849 Cov.: 32 AF XY: 0.517 AC XY: 38439 AN XY: 74282

African (AFR) AF: 0.339 AC: 14067 AN: 41450

American (AMR) AF: 0.639 AC: 9752 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2066 AN: 3468

East Asian (EAS) AF: 0.862 AC: 4462 AN: 5174

South Asian (SAS) AF: 0.645 AC: 3098 AN: 4806

European-Finnish (FIN) AF: 0.590 AC: 6219 AN: 10540

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35889 AN: 67962

Other (OTH) AF: 0.521 AC: 1097 AN: 2106

Alfa AF: 0.525 Hom.: 55878

Bravo AF: 0.504

Asia WGS AF: 0.717 AC: 2494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs4667622; hg19: chr2-171004185;