2-102548670-T-C

Variant names:

• chr2-102548670-T-C
• rs12712157

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 0.779 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.781

Alfa AF: 0.778 Hom.: 11399

Bravo AF: 0.778

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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