rs2146180

Variant names:

• chr9-8045606-G-A
• rs2146180

Your query was ambiguous. Multiple possible variants found:

• chr9-8045606-G-A
• chr9-8045606-G-T

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 0.607 in 151,758 control chromosomes in the GnomAD database, including 28,096 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 0.61 (28096 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.607 AC: 92055 AN: 151640 Hom.: 28063 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.607 AC: 92127 AN: 151758 Hom.: 28096 Cov.: 31 AF XY: 0.614 AC XY: 45491 AN XY: 74134

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.646

Alfa AF: 0.611 Hom.: 33694

Bravo AF: 0.604

Asia WGS AF: 0.684 AC: 2378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2146180; hg19: chr9-8045606; COSMIC: COSV69445769;