2-102548670-T-C

Variant names:

• chr2-102548670-T-C
• rs12712157

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 0.779 in 152,198 control chromosomes in the GnomAD database, including 46,555 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 0.78 (46555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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: 0.779 AC: 118446 AN: 152080 Hom.: 46506 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.779 AC: 118554 AN: 152198 Hom.: 46555 Cov.: 32 AF XY: 0.776 AC XY: 57721 AN XY: 74418

African (AFR) AF: 0.838 AC: 34797 AN: 41522

American (AMR) AF: 0.781 AC: 11934 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2514 AN: 3472

East Asian (EAS) AF: 0.540 AC: 2792 AN: 5174

South Asian (SAS) AF: 0.663 AC: 3201 AN: 4830

European-Finnish (FIN) AF: 0.808 AC: 8564 AN: 10602

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52205 AN: 67998

Other (OTH) AF: 0.781 AC: 1649 AN: 2112

Alfa AF: 0.775 Hom.: 17862

Bravo AF: 0.778

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs12712157; hg19: chr2-103165129; COSMIC: COSV60085997;