rs17861099

Variant names:

• chr15-74725999-C-T
• rs17861099

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0519 in 152,158 control chromosomes in the GnomAD database, including 280 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 0.052 (280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0520 AC: 7905 AN: 152040 Hom.: 281 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.000774

Gnomad SAS AF: 0.0282

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0519 AC: 7898 AN: 152158 Hom.: 280 Cov.: 32 AF XY: 0.0513 AC XY: 3812 AN XY: 74372

African (AFR) AF: 0.0124 AC: 517 AN: 41526

American (AMR) AF: 0.0440 AC: 672 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0763 AC: 265 AN: 3472

East Asian (EAS) AF: 0.000775 AC: 4 AN: 5158

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4820

European-Finnish (FIN) AF: 0.0959 AC: 1018 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0751 AC: 5107 AN: 67960

Other (OTH) AF: 0.0610 AC: 129 AN: 2116

Alfa AF: 0.0592 Hom.: 90

Bravo AF: 0.0474

Asia WGS AF: 0.00722 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.4
DANN	Benign	0.84
PhyloP100		-1.0
PromoterAI		0.0076	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17861099; hg19: chr15-75018340;