10-95069673-G-T

Position:

• chr10-95069673-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.182 in 152,112 control chromosomes in the GnomAD database, including 3,221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.18 (3221 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 10-95069673-G-T is Benign according to our data. Variant chr10-95069673-G-T is described in Lovd as [Likely_benign]. Variant chr10-95069673-G-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95069673G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27700 AN: 151994 Hom.: 3216 Cov.: 32

Gnomad AFR AF: 0.0447

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.182 AC: 27704 AN: 152112 Hom.: 3221 Cov.: 32 AF XY: 0.185 AC XY: 13772 AN XY: 74354

Gnomad4 AFR AF: 0.0446

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0850

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.163

Alfa AF: 0.221 Hom.: 7995

Bravo AF: 0.170

Asia WGS AF: 0.118 AC: 411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7909236; hg19: chr10-96829430;