chr2-137775186-T-C

Variant names:

• chr2-137775186-T-C
• rs2925216

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 0.82 in 151,928 control chromosomes in the GnomAD database, including 52,743 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 0.82 (52743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 5 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 = 0.936 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124570 AN: 151810 Hom.: 52709 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.820 AC: 124655 AN: 151928 Hom.: 52743 Cov.: 32 AF XY: 0.818 AC XY: 60724 AN XY: 74248

African (AFR) AF: 0.656 AC: 27177 AN: 41444

American (AMR) AF: 0.754 AC: 11480 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3025 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2225 AN: 5100

South Asian (SAS) AF: 0.783 AC: 3777 AN: 4822

European-Finnish (FIN) AF: 0.959 AC: 10185 AN: 10624

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.942 AC: 63971 AN: 67918

Other (OTH) AF: 0.806 AC: 1702 AN: 2112

Alfa AF: 0.847 Hom.: 9110

Bravo AF: 0.793

Asia WGS AF: 0.646 AC: 2247 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.71
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2925216; hg19: chr2-138532756; COSMIC: COSV70042900;