rs10503148

chr8-613664-C-T

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 0.0588 in 152,182 control chromosomes in the GnomAD database, including 290 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 0.059 (290 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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 (AMR) allele frequency at 95% confidence interval = 0.067 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: 0.0589 AC: 8949 AN: 152062 Hom.: 291 Cov.: 33

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.0355

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0588 AC: 8952 AN: 152182 Hom.: 290 Cov.: 33 AF XY: 0.0611 AC XY: 4549 AN XY: 74408

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.0355

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.0545

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0572 Hom.: 36

Bravo AF: 0.0579

Asia WGS AF: 0.0490 AC: 172 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	5.7
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503148; hg19: chr8-563664;