12-90513117-T-A

Variant names:

• chr12-90513117-T-A
• rs10506988

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 0.517 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.839 AC: 34778 AN: 41464

American (AMR) AF: 0.468 AC: 7114 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3466

East Asian (EAS) AF: 0.665 AC: 3423 AN: 5144

South Asian (SAS) AF: 0.442 AC: 2129 AN: 4814

European-Finnish (FIN) AF: 0.335 AC: 3541 AN: 10576

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25070 AN: 67828

Other (OTH) AF: 0.456 AC: 964 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10506988; hg19: chr12-90906894;