chr10-69269546-T-G

Position:

• chr10-69269546-T-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 0.181 in 152,260 control chromosomes in the GnomAD database, including 2,993 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 0.18 (2993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27596 AN: 152142 Hom.: 2995 Cov.: 32

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.181 AC: 27595 AN: 152260 Hom.: 2993 Cov.: 32 AF XY: 0.183 AC XY: 13590 AN XY: 74448

Gnomad4 AFR AF: 0.0791

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0784

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.164

Alfa AF: 0.188 Hom.: 299

Bravo AF: 0.169

Asia WGS AF: 0.131 AC: 459 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	1.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2394534; hg19: chr10-71029302;