10-93161308-A-G

Position:

• chr10-93161308-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 0.152 in 152,188 control chromosomes in the GnomAD database, including 3,914 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 0.15 (3914 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93161308A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23146 AN: 152070 Hom.: 3904 Cov.: 32

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.152 AC: 23165 AN: 152188 Hom.: 3914 Cov.: 32 AF XY: 0.164 AC XY: 12236 AN XY: 74390

Gnomad4 AFR AF: 0.0384

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.136

Alfa AF: 0.128 Hom.: 2187

Bravo AF: 0.161

Asia WGS AF: 0.542 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4918664; hg19: chr10-94921065;