rs2491649

Variant names:

• chr9-126266231-G-A
• rs2491649

Your query was ambiguous. Multiple possible variants found:

• chr9-126266231-G-A
• chr9-126266231-G-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 0.596 in 151,868 control chromosomes in the GnomAD database, including 27,127 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 (27127 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 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: 0.596 AC: 90440 AN: 151750 Hom.: 27125 Cov.: 31

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.596 AC: 90481 AN: 151868 Hom.: 27127 Cov.: 31 AF XY: 0.597 AC XY: 44307 AN XY: 74222

African (AFR) AF: 0.556 AC: 23032 AN: 41416

American (AMR) AF: 0.564 AC: 8599 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2343 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2377 AN: 5162

South Asian (SAS) AF: 0.714 AC: 3424 AN: 4798

European-Finnish (FIN) AF: 0.631 AC: 6641 AN: 10530

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42101 AN: 67934

Other (OTH) AF: 0.586 AC: 1231 AN: 2100

Alfa AF: 0.605 Hom.: 4848

Bravo AF: 0.587

Asia WGS AF: 0.572 AC: 1990 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.73
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs2491649; hg19: chr9-129028510;