rs10503840

chr8-29397384-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 0.0393 in 152,194 control chromosomes in the GnomAD database, including 176 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 0.039 (176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0587 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: 0.0393 AC: 5980 AN: 152076 Hom.: 176 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0271

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0457

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0603

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0393 AC: 5980 AN: 152194 Hom.: 176 Cov.: 32 AF XY: 0.0385 AC XY: 2863 AN XY: 74410

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0830

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0373

Gnomad4 NFE AF: 0.0603

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0562 Hom.: 123

Bravo AF: 0.0375

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	7.8
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: rs10503840; hg19: chr8-29254901;