chr10-68252081-A-G

Position:

• chr10-68252081-A-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 0.332 in 152,016 control chromosomes in the GnomAD database, including 8,917 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 0.33 (8917 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.68252081A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50425 AN: 151898 Hom.: 8902 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.332 AC: 50478 AN: 152016 Hom.: 8917 Cov.: 32 AF XY: 0.338 AC XY: 25117 AN XY: 74318

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.301

Alfa AF: 0.281 Hom.: 14483

Bravo AF: 0.344

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	10
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3858145; hg19: chr10-70011838;