12-112901622-T-C

Variant names:

• chr12-112901622-T-C
• rs10774669

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 0.752 in 152,126 control chromosomes in the GnomAD database, including 43,622 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 0.75 (43622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.752 AC: 114360 AN: 152008 Hom.: 43610 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.752 AC: 114428 AN: 152126 Hom.: 43622 Cov.: 32 AF XY: 0.755 AC XY: 56130 AN XY: 74376

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.771

Alfa AF: 0.747 Hom.: 5781

Bravo AF: 0.752

Asia WGS AF: 0.821 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10774669; hg19: chr12-113339427;