rs9291163

Variant names:

• chr4-71833988-T-C
• rs9291163

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 0.522 in 151,934 control chromosomes in the GnomAD database, including 21,410 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 0.52 (21410 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 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: 0.522 AC: 79228 AN: 151816 Hom.: 21403 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.522 AC: 79267 AN: 151934 Hom.: 21410 Cov.: 31 AF XY: 0.520 AC XY: 38599 AN XY: 74254

African (AFR) AF: 0.421 AC: 17443 AN: 41442

American (AMR) AF: 0.606 AC: 9252 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3468

East Asian (EAS) AF: 0.274 AC: 1412 AN: 5156

South Asian (SAS) AF: 0.521 AC: 2506 AN: 4812

European-Finnish (FIN) AF: 0.524 AC: 5522 AN: 10544

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39181 AN: 67936

Other (OTH) AF: 0.534 AC: 1129 AN: 2114

Alfa AF: 0.558 Hom.: 93088

Bravo AF: 0.518

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.25
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs9291163; hg19: chr4-72699705;