rs1871692

Variant names:

• chr9-113738997-A-C
• rs1871692

Your query was ambiguous. Multiple possible variants found:

• chr9-113738997-A-C
• chr9-113738997-A-T

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 0.387 in 151,960 control chromosomes in the GnomAD database, including 12,683 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 0.39 (12683 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.387 AC: 58715 AN: 151842 Hom.: 12629 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.387 AC: 58835 AN: 151960 Hom.: 12683 Cov.: 31 AF XY: 0.395 AC XY: 29325 AN XY: 74286

African (AFR) AF: 0.515 AC: 21348 AN: 41422

American (AMR) AF: 0.490 AC: 7480 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3472

East Asian (EAS) AF: 0.679 AC: 3504 AN: 5164

South Asian (SAS) AF: 0.359 AC: 1733 AN: 4822

European-Finnish (FIN) AF: 0.357 AC: 3772 AN: 10564

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18395 AN: 67932

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.303 Hom.: 12631

Bravo AF: 0.410

Asia WGS AF: 0.493 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.9
DANN	Benign	0.91
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1871692; hg19: chr9-116501277;