rs10504663

Positions:

• chr8-77956444-A-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 0.249 in 152,138 control chromosomes in the GnomAD database, including 5,314 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 0.25 (5314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37826 AN: 152020 Hom.: 5311 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.249 AC: 37839 AN: 152138 Hom.: 5314 Cov.: 32 AF XY: 0.248 AC XY: 18452 AN XY: 74380

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.270

Alfa AF: 0.271 Hom.: 737

Bravo AF: 0.239

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.52
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504663; hg19: chr8-78868679;