rs2151641

Variant names:

• chr9-119804081-G-A
• rs2151641

Your query was ambiguous. Multiple possible variants found:

• chr9-119804081-G-A
• chr9-119804081-G-C

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 0.198 in 152,080 control chromosomes in the GnomAD database, including 3,197 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 (3197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.894

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 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: 0.198 AC: 30140 AN: 151964 Hom.: 3196 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.198 AC: 30182 AN: 152080 Hom.: 3197 Cov.: 32 AF XY: 0.195 AC XY: 14519 AN XY: 74342

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.00310

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.197

Alfa AF: 0.207 Hom.: 4603

Bravo AF: 0.189

Asia WGS AF: 0.161 AC: 557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2151641; hg19: chr9-122566359;