12-126508343-G-C

Variant names:

• chr12-126508343-G-C
• rs10492049

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 0.0628 in 149,964 control chromosomes in the GnomAD database, including 319 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 0.063 (319 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0834 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: 0.0627 AC: 9404 AN: 149892 Hom.: 320 Cov.: 31

Gnomad AFR AF: 0.0857

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.0266

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.0638

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

GnomAD4 genome AF: 0.0628 AC: 9414 AN: 149964 Hom.: 319 Cov.: 31 AF XY: 0.0626 AC XY: 4579 AN XY: 73128

African (AFR) AF: 0.0858 AC: 3500 AN: 40796

American (AMR) AF: 0.0557 AC: 838 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 297 AN: 3460

East Asian (EAS) AF: 0.0267 AC: 136 AN: 5096

South Asian (SAS) AF: 0.0524 AC: 248 AN: 4732

European-Finnish (FIN) AF: 0.0452 AC: 448 AN: 9906

Middle Eastern (MID) AF: 0.108 AC: 31 AN: 288

European-Non Finnish (NFE) AF: 0.0546 AC: 3694 AN: 67648

Other (OTH) AF: 0.0637 AC: 133 AN: 2088

Alfa AF: 0.0142 Hom.: 4

Bravo AF: 0.0651

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.44
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10492049; hg19: chr12-126992889;