10-69692529-T-C

Position:

• chr10-69692529-T-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 0.86 in 152,368 control chromosomes in the GnomAD database, including 56,454 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 0.86 (56420 hom., cov: 33)
  • Exomes 𝑓: 0.90 (34 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69692529T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130830 AN: 152164 Hom.: 56364 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.876

GnomAD4 exome AF: 0.895 AC: 77 AN: 86 Hom.: 34 AF XY: 0.914 AC XY: 53 AN XY: 58

Gnomad4 AFR exome AF: 0.833

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.906

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.860 AC: 130946 AN: 152282 Hom.: 56420 Cov.: 33 AF XY: 0.860 AC XY: 64054 AN XY: 74480

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.930

Gnomad4 SAS AF: 0.878

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.877

Alfa AF: 0.843 Hom.: 73073

Bravo AF: 0.868

Asia WGS AF: 0.887 AC: 3082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0040
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2812533; hg19: chr10-71452285;