9-105892815-G-T

Variant names:

• chr9-105892815-G-T
• rs4742971

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 0.0909 in 152,094 control chromosomes in the GnomAD database, including 1,343 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 0.091 (1343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 4 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 = 0.493 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: 0.0909 AC: 13812 AN: 151978 Hom.: 1334 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0326

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0909 AC: 13826 AN: 152094 Hom.: 1343 Cov.: 32 AF XY: 0.0930 AC XY: 6914 AN XY: 74334

African (AFR) AF: 0.0278 AC: 1155 AN: 41518

American (AMR) AF: 0.187 AC: 2860 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2618 AN: 5136

South Asian (SAS) AF: 0.129 AC: 621 AN: 4802

European-Finnish (FIN) AF: 0.0326 AC: 346 AN: 10612

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0777 AC: 5280 AN: 67990

Other (OTH) AF: 0.112 AC: 236 AN: 2108

Alfa AF: 0.0971 Hom.: 3828

Bravo AF: 0.104

Asia WGS AF: 0.304 AC: 1055 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	2.2
DANN	Benign	0.64
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs4742971; hg19: chr9-108655096;