rs10867025

Positions:

• chr8-7051919-C-T

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 0.355 in 152,092 control chromosomes in the GnomAD database, including 9,907 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 0.36 (9907 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.373

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7051919C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53970 AN: 151974 Hom.: 9904 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.355 AC: 54003 AN: 152092 Hom.: 9907 Cov.: 33 AF XY: 0.358 AC XY: 26663 AN XY: 74374

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.364

Alfa AF: 0.388 Hom.: 5355

Bravo AF: 0.348

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.76
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10867025; hg19: chr8-6909441;