chr9-27581982-G-T

Variant names:

• chr9-27581982-G-T
• rs10967992

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 0.204 in 152,030 control chromosomes in the GnomAD database, including 3,532 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 0.20 (3532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 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: 0.204 AC: 31041 AN: 151912 Hom.: 3528 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.204 AC: 31054 AN: 152030 Hom.: 3532 Cov.: 32 AF XY: 0.202 AC XY: 14996 AN XY: 74294

African (AFR) AF: 0.121 AC: 5006 AN: 41492

American (AMR) AF: 0.162 AC: 2480 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 872 AN: 3466

East Asian (EAS) AF: 0.103 AC: 533 AN: 5166

South Asian (SAS) AF: 0.206 AC: 989 AN: 4810

European-Finnish (FIN) AF: 0.251 AC: 2644 AN: 10550

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17934 AN: 67952

Other (OTH) AF: 0.200 AC: 421 AN: 2106

Alfa AF: 0.234 Hom.: 5395

Bravo AF: 0.190

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.077
DANN	Benign	0.66
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10967992; hg19: chr9-27581980; COSMIC: COSV69455392;