chr9-111097031-G-C

Variant names:

• chr9-111097031-G-C
• rs2014343

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 0.304 in 152,058 control chromosomes in the GnomAD database, including 7,485 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 0.30 (7485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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: 0.304 AC: 46156 AN: 151940 Hom.: 7484 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.304 AC: 46165 AN: 152058 Hom.: 7485 Cov.: 32 AF XY: 0.312 AC XY: 23212 AN XY: 74318

African (AFR) AF: 0.219 AC: 9070 AN: 41488

American (AMR) AF: 0.345 AC: 5276 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3468

East Asian (EAS) AF: 0.434 AC: 2236 AN: 5150

South Asian (SAS) AF: 0.492 AC: 2370 AN: 4814

European-Finnish (FIN) AF: 0.381 AC: 4021 AN: 10566

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20751 AN: 67978

Other (OTH) AF: 0.319 AC: 674 AN: 2114

Alfa AF: 0.163 Hom.: 342

Bravo AF: 0.296

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2014343; hg19: chr9-113859311; COSMIC: COSV66913032;