rs10444801

chr15-55109840-G-Achr15-55109840-G-Cchr15-55109840-G-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 0.771 in 151,990 control chromosomes in the GnomAD database, including 46,366 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 0.77 (46366 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 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: 0.771 AC: 117150 AN: 151870 Hom.: 46357 Cov.: 30

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.771 AC: 117201 AN: 151990 Hom.: 46366 Cov.: 30 AF XY: 0.776 AC XY: 57625 AN XY: 74292

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.803

Alfa AF: 0.812 Hom.: 17185

Bravo AF: 0.764

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	6.7
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10444801; hg19: chr15-55402038;