rs17100108

Variant names:

• chr14-62591894-A-T
• rs17100108

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 0.125 in 151,990 control chromosomes in the GnomAD database, including 1,619 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 0.13 (1619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.963
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.161 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: 0.125 AC: 19028 AN: 151872 Hom.: 1618 Cov.: 32

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.125 AC: 19031 AN: 151990 Hom.: 1619 Cov.: 32 AF XY: 0.127 AC XY: 9460 AN XY: 74276

African (AFR) AF: 0.0314 AC: 1305 AN: 41534

American (AMR) AF: 0.137 AC: 2086 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3464

East Asian (EAS) AF: 0.0537 AC: 278 AN: 5180

South Asian (SAS) AF: 0.145 AC: 700 AN: 4822

European-Finnish (FIN) AF: 0.238 AC: 2513 AN: 10556

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11109 AN: 67896

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.162 Hom.: 306

Bravo AF: 0.112

Asia WGS AF: 0.110 AC: 380 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	14
DANN	Benign	0.76
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs17100108; hg19: chr14-63058612;