rs2737190

Variant names:

• chr9-117701903-G-A
• rs2737190

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 0.531 in 151,970 control chromosomes in the GnomAD database, including 24,123 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 0.53 (24123 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 58 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80740 AN: 151852 Hom.: 24129 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.531 AC: 80750 AN: 151970 Hom.: 24123 Cov.: 31 AF XY: 0.530 AC XY: 39366 AN XY: 74288

African (AFR) AF: 0.234 AC: 9698 AN: 41434

American (AMR) AF: 0.614 AC: 9373 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3186 AN: 5140

South Asian (SAS) AF: 0.617 AC: 2976 AN: 4822

European-Finnish (FIN) AF: 0.550 AC: 5818 AN: 10574

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45411 AN: 67950

Other (OTH) AF: 0.580 AC: 1227 AN: 2114

Alfa AF: 0.591 Hom.: 4497

Bravo AF: 0.527

Asia WGS AF: 0.594 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.68
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2737190; hg19: chr9-120464181;