rs2081381

Variant names:

• chr9-21148600-C-G
• rs2081381

Your query was ambiguous. Multiple possible variants found:

• chr9-21148600-C-G
• chr9-21148600-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 0.598 in 151,896 control chromosomes in the GnomAD database, including 27,201 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 0.60 (27201 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.622 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: 0.598 AC: 90760 AN: 151778 Hom.: 27178 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.598 AC: 90831 AN: 151896 Hom.: 27201 Cov.: 31 AF XY: 0.595 AC XY: 44175 AN XY: 74248

African (AFR) AF: 0.576 AC: 23832 AN: 41410

American (AMR) AF: 0.627 AC: 9588 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3468

East Asian (EAS) AF: 0.533 AC: 2752 AN: 5164

South Asian (SAS) AF: 0.641 AC: 3085 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5641 AN: 10522

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41792 AN: 67924

Other (OTH) AF: 0.605 AC: 1277 AN: 2112

Alfa AF: 0.457 Hom.: 1191

Bravo AF: 0.601

Asia WGS AF: 0.624 AC: 2168 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	0.83
DANN	Benign	0.67
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2081381; hg19: chr9-21148599; COSMIC: COSV69450661;