rs9291163

Positions:

• chr4-71833988-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.534

Alfa AF: 0.567 Hom.: 45069

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9291163; hg19: chr4-72699705;