rs17114247

Variant names:

• chr21-42058026-C-T
• rs17114247

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 0.117 in 152,130 control chromosomes in the GnomAD database, including 1,549 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 0.12 (1549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 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: 0.117 AC: 17814 AN: 152012 Hom.: 1543 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0669

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.117 AC: 17846 AN: 152130 Hom.: 1549 Cov.: 32 AF XY: 0.117 AC XY: 8737 AN XY: 74376

African (AFR) AF: 0.243 AC: 10075 AN: 41454

American (AMR) AF: 0.0668 AC: 1023 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5164

South Asian (SAS) AF: 0.114 AC: 547 AN: 4810

European-Finnish (FIN) AF: 0.0650 AC: 688 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0554 AC: 3765 AN: 68020

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.0767 Hom.: 2588

Bravo AF: 0.125

Asia WGS AF: 0.133 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.86
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs17114247; hg19: chr21-43478135;