rs818704

Positions:

• chr9-113386036-G-A
• chr9-113386036-G-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 0.109 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0259

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.118

Alfa AF: 0.134 Hom.: 896

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs818704; hg19: chr9-116148316;