rs2737191

Variant names:

• chr9-117700437-A-G
• rs2737191

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 0.22 in 152,152 control chromosomes in the GnomAD database, including 4,102 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 0.22 (4102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 35 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 = 0.277 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33441 AN: 152034 Hom.: 4101 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.220 AC: 33449 AN: 152152 Hom.: 4102 Cov.: 32 AF XY: 0.217 AC XY: 16113 AN XY: 74392

African (AFR) AF: 0.137 AC: 5683 AN: 41524

American (AMR) AF: 0.224 AC: 3427 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5172

South Asian (SAS) AF: 0.219 AC: 1056 AN: 4822

European-Finnish (FIN) AF: 0.232 AC: 2459 AN: 10582

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19091 AN: 67980

Other (OTH) AF: 0.235 AC: 495 AN: 2108

Alfa AF: 0.259 Hom.: 17460

Bravo AF: 0.217

Asia WGS AF: 0.104 AC: 364 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	6.0
DANN	Benign	0.66
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs2737191; hg19: chr9-120462715; COSMIC: COSV62922748;