rs10503669

Variant names:

• chr8-19990179-C-A
• rs10503669

Your query was ambiguous. Multiple possible variants found:

• chr8-19990179-C-A
• chr8-19990179-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 0.085 in 152,124 control chromosomes in the GnomAD database, including 561 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 0.085 (561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 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: 0.0851 AC: 12939 AN: 152006 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0600

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0981

Gnomad OTH AF: 0.0843

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

GnomAD4 genome AF: 0.0850 AC: 12928 AN: 152124 Hom.: 561 Cov.: 32 AF XY: 0.0842 AC XY: 6259 AN XY: 74352

Gnomad4 AFR AF: 0.0599

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.0995

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.0881

Gnomad4 NFE AF: 0.0981

Gnomad4 OTH AF: 0.0834

Alfa AF: 0.0923 Hom.: 1002

Bravo AF: 0.0818

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503669; hg19: chr8-19847690;