rs10748087

Positions:

• chr12-67801315-C-G
• chr12-67801315-C-T

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 0.534 in 151,620 control chromosomes in the GnomAD database, including 21,829 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 (21829 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.534 AC: 80837 AN: 151506 Hom.: 21806 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.534 AC: 80909 AN: 151620 Hom.: 21829 Cov.: 31 AF XY: 0.529 AC XY: 39152 AN XY: 74076

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.520

Alfa AF: 0.565 Hom.: 2942

Bravo AF: 0.524

Asia WGS AF: 0.472 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.43
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10748087; hg19: chr12-68195095;