chr12-107163839-C-T

Variant names:

• chr12-107163839-C-T
• rs10437896

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 0.125 in 152,116 control chromosomes in the GnomAD database, including 1,889 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 0.13 (1889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 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: 0.125 AC: 19011 AN: 151998 Hom.: 1878 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0338

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.125 AC: 19065 AN: 152116 Hom.: 1889 Cov.: 32 AF XY: 0.128 AC XY: 9520 AN XY: 74368

African (AFR) AF: 0.255 AC: 10561 AN: 41494

American (AMR) AF: 0.137 AC: 2100 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0338 AC: 117 AN: 3466

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5168

South Asian (SAS) AF: 0.154 AC: 743 AN: 4828

European-Finnish (FIN) AF: 0.0524 AC: 555 AN: 10590

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3246 AN: 67980

Other (OTH) AF: 0.106 AC: 223 AN: 2108

Alfa AF: 0.0726 Hom.: 358

Bravo AF: 0.137

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.1
DANN	Benign	0.91
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10437896; hg19: chr12-107557617;