chr9-111805480-T-C

Variant names:

• chr9-111805480-T-C
• rs667463

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 0.518 in 151,974 control chromosomes in the GnomAD database, including 21,775 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 0.52 (21775 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.518 AC: 78599 AN: 151856 Hom.: 21749 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.518 AC: 78669 AN: 151974 Hom.: 21775 Cov.: 31 AF XY: 0.529 AC XY: 39315 AN XY: 74280

African (AFR) AF: 0.337 AC: 13976 AN: 41440

American (AMR) AF: 0.654 AC: 9994 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1898 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4502 AN: 5162

South Asian (SAS) AF: 0.559 AC: 2686 AN: 4806

European-Finnish (FIN) AF: 0.631 AC: 6652 AN: 10548

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.547 AC: 37174 AN: 67950

Other (OTH) AF: 0.524 AC: 1108 AN: 2114

Alfa AF: 0.537 Hom.: 37790

Bravo AF: 0.514

Asia WGS AF: 0.677 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs667463; hg19: chr9-114567760; COSMIC: COSV70058496;