9-113598691-C-G

Variant names:

• chr9-113598691-C-G
• rs944343

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 0.778 in 152,184 control chromosomes in the GnomAD database, including 46,432 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 0.78 (46432 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 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: 0.778 AC: 118298 AN: 152066 Hom.: 46397 Cov.: 33

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.778 AC: 118385 AN: 152184 Hom.: 46432 Cov.: 33 AF XY: 0.782 AC XY: 58211 AN XY: 74398

African (AFR) AF: 0.850 AC: 35284 AN: 41530

American (AMR) AF: 0.809 AC: 12380 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2539 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5110 AN: 5176

South Asian (SAS) AF: 0.833 AC: 4014 AN: 4818

European-Finnish (FIN) AF: 0.737 AC: 7815 AN: 10600

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48599 AN: 67972

Other (OTH) AF: 0.778 AC: 1646 AN: 2116

Alfa AF: 0.743 Hom.: 5247

Bravo AF: 0.789

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.23
DANN	Benign	0.66
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs944343; hg19: chr9-116360971; COSMIC: COSV59521518;