rs10508402

chr10-9133493-G-A

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 0.0305 in 129,862 control chromosomes in the GnomAD database, including 141 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 0.030 (141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.11 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: 0.0304 AC: 3940 AN: 129784 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.00789

Gnomad AMI AF: 0.00489

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.00561

Gnomad EAS AF: 0.00306

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0265

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

GnomAD4 genome AF: 0.0305 AC: 3956 AN: 129862 Hom.: 141 Cov.: 31 AF XY: 0.0323 AC XY: 2053 AN XY: 63616

Gnomad4 AFR AF: 0.00787

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.00561

Gnomad4 EAS AF: 0.00307

Gnomad4 SAS AF: 0.0169

Gnomad4 FIN AF: 0.0288

Gnomad4 NFE AF: 0.0288

Gnomad4 OTH AF: 0.0261

Alfa AF: 0.0261 Hom.: 12

Bravo AF: 0.0312

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508402; hg19: chr10-9175456;