rs2491649

Positions:

• chr9-126266231-G-A
• chr9-126266231-G-T

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 0.596 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.586

Alfa AF: 0.606 Hom.: 4736

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2491649; hg19: chr9-129028510;