rs10115381

Positions:

• chr9-26007602-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0164 in 152,234 control chromosomes in the GnomAD database, including 69 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 0.016 (69 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0164 (2496/152234) while in subpopulation AFR AF= 0.0495 (2059/41568). AF 95% confidence interval is 0.0478. There are 69 homozygotes in gnomad4. There are 1226 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 69 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26007602T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0164 AC: 2488 AN: 152116 Hom.: 68 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00853

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0271

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00103

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0164 AC: 2496 AN: 152234 Hom.: 69 Cov.: 32 AF XY: 0.0165 AC XY: 1226 AN XY: 74422

Gnomad4 AFR AF: 0.0495

Gnomad4 AMR AF: 0.00852

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0273

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.000282

Gnomad4 NFE AF: 0.00103

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.00953 Hom.: 2

Bravo AF: 0.0184

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10115381; hg19: chr9-26007600;