10-94761817-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 0.0683 in 152,260 control chromosomes in the GnomAD database, including 413 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 0.068 (413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0683 AC: 10386 AN: 152142 Hom.: 410 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0678

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

GnomAD4 genome AF: 0.0683 AC: 10392 AN: 152260 Hom.: 413 Cov.: 32 AF XY: 0.0685 AC XY: 5098 AN XY: 74444

Gnomad4 AFR AF: 0.0758

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0511

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.0699

Alfa AF: 0.0390 Hom.: 30

Bravo AF: 0.0665

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11568732; hg19: chr10-96521574;