12-112904357-A-G

Variant names:

• chr12-112904357-A-G
• rs10774670

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 0.653 in 152,004 control chromosomes in the GnomAD database, including 34,459 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 0.65 (34459 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 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: 0.654 AC: 99310 AN: 151886 Hom.: 34467 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.653 AC: 99327 AN: 152004 Hom.: 34459 Cov.: 31 AF XY: 0.657 AC XY: 48785 AN XY: 74296

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.680

Alfa AF: 0.703 Hom.: 4828

Bravo AF: 0.644

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10774670; hg19: chr12-113342162;