chr9-120192965-G-T

Variant names:

• chr9-120192965-G-T
• rs1156214

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 0.681 in 152,086 control chromosomes in the GnomAD database, including 36,020 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 0.68 (36020 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103449 AN: 151968 Hom.: 36002 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.681 AC: 103511 AN: 152086 Hom.: 36020 Cov.: 32 AF XY: 0.679 AC XY: 50477 AN XY: 74352

African (AFR) AF: 0.526 AC: 21817 AN: 41460

American (AMR) AF: 0.695 AC: 10618 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2622 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3939 AN: 5174

South Asian (SAS) AF: 0.628 AC: 3022 AN: 4814

European-Finnish (FIN) AF: 0.704 AC: 7446 AN: 10572

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51778 AN: 67988

Other (OTH) AF: 0.699 AC: 1480 AN: 2116

Alfa AF: 0.720 Hom.: 30305

Bravo AF: 0.672

Asia WGS AF: 0.664 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.039
DANN	Benign	0.26
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1156214; hg19: chr9-122955243; COSMIC: COSV60400678;