rs10459511

Variant names:

• chr14-55800098-G-A
• rs10459511

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 0.0779 in 152,294 control chromosomes in the GnomAD database, including 802 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 0.078 (802 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 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: 0.0779 AC: 11858 AN: 152176 Hom.: 802 Cov.: 33

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0779 AC: 11860 AN: 152294 Hom.: 802 Cov.: 33 AF XY: 0.0808 AC XY: 6015 AN XY: 74474

Gnomad4 AFR AF: 0.0179

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.0874

Alfa AF: 0.0772 Hom.: 776

Bravo AF: 0.0889

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10459511; hg19: chr14-56266816;