rs10504069

Variant names:

• chr8-49038251-T-A
• rs10504069

Your query was ambiguous. Multiple possible variants found:

• chr8-49038251-T-A
• chr8-49038251-T-C
• chr8-49038251-T-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 0.188 in 152,226 control chromosomes in the GnomAD database, including 3,628 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 0.19 (3628 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.492 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: 0.188 AC: 28584 AN: 152108 Hom.: 3609 Cov.: 33

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.188 AC: 28620 AN: 152226 Hom.: 3628 Cov.: 33 AF XY: 0.195 AC XY: 14520 AN XY: 74442

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.186

Alfa AF: 0.190 Hom.: 419

Bravo AF: 0.193

Asia WGS AF: 0.432 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504069; hg19: chr8-49950810;