rs10770291

Positions:

• chr12-17955114-G-C

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 0.572 in 151,820 control chromosomes in the GnomAD database, including 25,862 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 0.57 (25862 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17955114G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86853 AN: 151702 Hom.: 25857 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.572 AC: 86882 AN: 151820 Hom.: 25862 Cov.: 30 AF XY: 0.582 AC XY: 43167 AN XY: 74206

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.554

Alfa AF: 0.588 Hom.: 3318

Bravo AF: 0.545

Asia WGS AF: 0.679 AC: 2361 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	1.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10770291; hg19: chr12-18108048; COSMIC: COSV50091539;