rs2381413

Variant names:

• chr9-6167017-C-G
• rs2381413

Your query was ambiguous. Multiple possible variants found:

• chr9-6167017-C-G
• chr9-6167017-C-T

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 0.465 in 151,924 control chromosomes in the GnomAD database, including 17,152 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 0.47 (17152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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: 0.465 AC: 70631 AN: 151808 Hom.: 17116 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.465 AC: 70720 AN: 151924 Hom.: 17152 Cov.: 32 AF XY: 0.466 AC XY: 34574 AN XY: 74222

African (AFR) AF: 0.601 AC: 24912 AN: 41420

American (AMR) AF: 0.437 AC: 6672 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1375 AN: 5144

South Asian (SAS) AF: 0.394 AC: 1895 AN: 4810

European-Finnish (FIN) AF: 0.450 AC: 4733 AN: 10524

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28160 AN: 67972

Other (OTH) AF: 0.453 AC: 957 AN: 2112

Alfa AF: 0.262 Hom.: 527

Bravo AF: 0.474

Asia WGS AF: 0.362 AC: 1260 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	0.72
DANN	Benign	0.51
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2381413; hg19: chr9-6167017;