9-120192965-G-T

Variant names:

• chr9-120192965-G-T
• rs1156214

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.681 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

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.699

Alfa AF: 0.720 Hom.: 21483

Bravo AF: 0.672

Asia WGS AF: 0.664 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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