rs818704

Variant names:

• chr9-113386036-G-A
• rs818704

Your query was ambiguous. Multiple possible variants found:

• chr9-113386036-G-A
• chr9-113386036-G-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 0.109 in 152,276 control chromosomes in the GnomAD database, including 1,164 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 0.11 (1164 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.168 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: 0.109 AC: 16604 AN: 152158 Hom.: 1164 Cov.: 33

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.109 AC: 16600 AN: 152276 Hom.: 1164 Cov.: 33 AF XY: 0.110 AC XY: 8177 AN XY: 74452

African (AFR) AF: 0.0259 AC: 1079 AN: 41584

American (AMR) AF: 0.111 AC: 1700 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3468

East Asian (EAS) AF: 0.154 AC: 796 AN: 5174

South Asian (SAS) AF: 0.178 AC: 859 AN: 4830

European-Finnish (FIN) AF: 0.119 AC: 1265 AN: 10592

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9659 AN: 68024

Other (OTH) AF: 0.118 AC: 250 AN: 2110

Alfa AF: 0.134 Hom.: 986

Bravo AF: 0.107

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs818704; hg19: chr9-116148316;