rs2151641

Positions:

• 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.894

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.119804081G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;