chr8-613664-C-T

Variant names:

• chr8-613664-C-T
• rs10503148

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;