rs10504856

chr8-87760559-T-C

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 0.234 in 152,178 control chromosomes in the GnomAD database, including 4,972 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 0.23 (4972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721

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 (NFE) allele frequency at 95% confidence interval = 0.312 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: 0.234 AC: 35597 AN: 152060 Hom.: 4969 Cov.: 32

Gnomad AFR AF: 0.0897

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.234 AC: 35607 AN: 152178 Hom.: 4972 Cov.: 32 AF XY: 0.231 AC XY: 17201 AN XY: 74386

Gnomad4 AFR AF: 0.0896

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.252

Alfa AF: 0.271 Hom.: 2017

Bravo AF: 0.222

Asia WGS AF: 0.215 AC: 750 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	0.57
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504856; hg19: chr8-88772787;