chr9-113404876-A-T

Variant names:

• chr9-113404876-A-T
• rs818694

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 0.32 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.440 AC: 18214 AN: 41408

American (AMR) AF: 0.222 AC: 3386 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3466

East Asian (EAS) AF: 0.0482 AC: 250 AN: 5184

South Asian (SAS) AF: 0.150 AC: 722 AN: 4824

European-Finnish (FIN) AF: 0.352 AC: 3716 AN: 10548

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20826 AN: 67942

Other (OTH) AF: 0.281 AC: 593 AN: 2114

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
PhyloP100		0.36

Splicing

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

Other links and lift over

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