rs10506896

Variant names:

• chr12-83657336-T-A
• rs10506896

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 0.0277 in 152,070 control chromosomes in the GnomAD database, including 98 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 0.028 (98 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0842 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: 0.0277 AC: 4208 AN: 151952 Hom.: 98 Cov.: 32

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0165

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0277 AC: 4214 AN: 152070 Hom.: 98 Cov.: 32 AF XY: 0.0298 AC XY: 2217 AN XY: 74340

African (AFR) AF: 0.0369 AC: 1532 AN: 41522

American (AMR) AF: 0.0140 AC: 213 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0165 AC: 57 AN: 3464

East Asian (EAS) AF: 0.0910 AC: 467 AN: 5130

South Asian (SAS) AF: 0.0721 AC: 348 AN: 4826

European-Finnish (FIN) AF: 0.0552 AC: 586 AN: 10616

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0135 AC: 917 AN: 67954

Other (OTH) AF: 0.0256 AC: 54 AN: 2110

Alfa AF: 0.0203 Hom.: 4

Bravo AF: 0.0244

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.77
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs10506896; hg19: chr12-84051115;