12-109604543-A-G

Variant names:

• chr12-109604543-A-G
• rs10161126

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 0.495 in 151,988 control chromosomes in the GnomAD database, including 19,152 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 (19152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 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: 0.495 AC: 75205 AN: 151870 Hom.: 19135 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.495 AC: 75271 AN: 151988 Hom.: 19152 Cov.: 32 AF XY: 0.487 AC XY: 36172 AN XY: 74280

African (AFR) AF: 0.510 AC: 21110 AN: 41430

American (AMR) AF: 0.413 AC: 6303 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1882 AN: 3466

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5156

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4812

European-Finnish (FIN) AF: 0.458 AC: 4843 AN: 10584

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36261 AN: 67966

Other (OTH) AF: 0.528 AC: 1113 AN: 2106

Alfa AF: 0.507 Hom.: 17948

Bravo AF: 0.495

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.28
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs10161126; hg19: chr12-110042348; COSMIC: COSV50457796;