12-94886937-T-C

Variant names:

• chr12-94886937-T-C
• rs10777647

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 0.502 in 151,886 control chromosomes in the GnomAD database, including 19,803 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 0.50 (19803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 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: 0.502 AC: 76136 AN: 151768 Hom.: 19774 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.502 AC: 76198 AN: 151886 Hom.: 19803 Cov.: 31 AF XY: 0.505 AC XY: 37462 AN XY: 74246

African (AFR) AF: 0.632 AC: 26185 AN: 41422

American (AMR) AF: 0.585 AC: 8925 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2610 AN: 5166

South Asian (SAS) AF: 0.403 AC: 1933 AN: 4798

European-Finnish (FIN) AF: 0.437 AC: 4593 AN: 10514

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28819 AN: 67946

Other (OTH) AF: 0.509 AC: 1070 AN: 2104

Alfa AF: 0.450 Hom.: 26683

Bravo AF: 0.520

Asia WGS AF: 0.492 AC: 1694 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10777647; hg19: chr12-95280713;