rs17103282

Variant names:

• chr14-35415609-C-T
• rs17103282

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0345 in 152,328 control chromosomes in the GnomAD database, including 114 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 0.035 (114 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0345 (5258/152328) while in subpopulation AMR AF= 0.0425 (651/15300). AF 95% confidence interval is 0.0398. There are 114 homozygotes in gnomad4. There are 2423 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 114 gene

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: 0.0345 AC: 5246 AN: 152210 Hom.: 112 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0345 AC: 5258 AN: 152328 Hom.: 114 Cov.: 33 AF XY: 0.0325 AC XY: 2423 AN XY: 74480

Gnomad4 AFR AF: 0.0295

Gnomad4 AMR AF: 0.0425

Gnomad4 ASJ AF: 0.0861

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0405

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0385 Hom.: 31

Bravo AF: 0.0361

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17103282; hg19: chr14-35884815;