rs4974665

Variant names:

• chr4-2266728-A-G
• rs4974665

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 0.529 in 152,088 control chromosomes in the GnomAD database, including 22,289 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 0.53 (22289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.595 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: 0.530 AC: 80473 AN: 151970 Hom.: 22269 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.529 AC: 80528 AN: 152088 Hom.: 22289 Cov.: 33 AF XY: 0.529 AC XY: 39363 AN XY: 74370

African (AFR) AF: 0.421 AC: 17467 AN: 41460

American (AMR) AF: 0.568 AC: 8687 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1967 AN: 3472

East Asian (EAS) AF: 0.174 AC: 901 AN: 5182

South Asian (SAS) AF: 0.426 AC: 2052 AN: 4818

European-Finnish (FIN) AF: 0.627 AC: 6625 AN: 10572

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40768 AN: 67980

Other (OTH) AF: 0.549 AC: 1161 AN: 2114

Alfa AF: 0.575 Hom.: 14851

Bravo AF: 0.521

Asia WGS AF: 0.289 AC: 1007 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	5.4
DANN	Benign	0.61
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4974665; hg19: chr4-2268455;