rs10778537

Variant names:

• chr12-107144695-C-T
• rs10778537

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 0.421 in 152,064 control chromosomes in the GnomAD database, including 13,900 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 0.42 (13900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.883
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.481 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: 0.421 AC: 63936 AN: 151944 Hom.: 13883 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.421 AC: 63987 AN: 152064 Hom.: 13900 Cov.: 32 AF XY: 0.421 AC XY: 31330 AN XY: 74336

African (AFR) AF: 0.317 AC: 13130 AN: 41444

American (AMR) AF: 0.399 AC: 6095 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1184 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1861 AN: 5178

South Asian (SAS) AF: 0.375 AC: 1805 AN: 4812

European-Finnish (FIN) AF: 0.528 AC: 5589 AN: 10578

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 33005 AN: 67982

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.460 Hom.: 8560

Bravo AF: 0.404

Asia WGS AF: 0.352 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs10778537; hg19: chr12-107538473;