rs818694

chr9-113404876-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 0.32 in 151,966 control chromosomes in the GnomAD database, including 8,505 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 0.32 (8505 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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: 0.320 AC: 48633 AN: 151848 Hom.: 8494 Cov.: 31

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.320 AC: 48686 AN: 151966 Hom.: 8505 Cov.: 31 AF XY: 0.315 AC XY: 23427 AN XY: 74288

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.0482

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.281

Alfa AF: 0.329 Hom.: 1068

Bravo AF: 0.315

Asia WGS AF: 0.0980 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.7
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs818694; hg19: chr9-116167156; COSMIC: COSV52958384;