rs1871692

chr9-113738997-A-Cchr9-113738997-A-T

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 0.387 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.370

Alfa AF: 0.290 Hom.: 9033

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1871692; hg19: chr9-116501277;