chr12-108373556-C-A

Position:

• chr12-108373556-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.079 in 152,290 control chromosomes in the GnomAD database, including 770 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 0.079 (770 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

ACMG classification

Verdict is Benign. Variant got -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 = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 12027 AN: 152172 Hom.: 772 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0790 AC: 12029 AN: 152290 Hom.: 770 Cov.: 32 AF XY: 0.0830 AC XY: 6183 AN XY: 74476

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0917

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.0529 Hom.: 935

Bravo AF: 0.0779

Asia WGS AF: 0.204 AC: 705 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	4.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861905; hg19: chr12-108767333; COSMIC: COSV59268980;