rs10081169

Positions:

• chr6-46777651-T-G

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 0.12 in 151,968 control chromosomes in the GnomAD database, including 2,815 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 0.12 (2815 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46777651T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18236 AN: 151850 Hom.: 2801 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0861

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.120 AC: 18286 AN: 151968 Hom.: 2815 Cov.: 32 AF XY: 0.119 AC XY: 8807 AN XY: 74294

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.0603

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.0855

Gnomad4 FIN AF: 0.0129

Gnomad4 NFE AF: 0.0213

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0768 Hom.: 203

Bravo AF: 0.138

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10081169; hg19: chr6-46745388;