rs10506988

chr12-90513117-T-Achr12-90513117-T-Cchr12-90513117-T-G

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 0.517 in 151,816 control chromosomes in the GnomAD database, including 23,715 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 0.52 (23715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78332 AN: 151698 Hom.: 23663 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.517 AC: 78444 AN: 151816 Hom.: 23715 Cov.: 32 AF XY: 0.512 AC XY: 37998 AN XY: 74210

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.456

Alfa AF: 0.245 Hom.: 491

Bravo AF: 0.540

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.48
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506988; hg19: chr12-90906894;