rs17118382

Positions:

• chr14-83312834-T-C

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 0.0492 in 152,258 control chromosomes in the GnomAD database, including 281 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 0.049 (281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 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: 0.0492 AC: 7488 AN: 152140 Hom.: 282 Cov.: 33

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0339

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

GnomAD4 genome AF: 0.0492 AC: 7491 AN: 152258 Hom.: 281 Cov.: 33 AF XY: 0.0516 AC XY: 3843 AN XY: 74442

Gnomad4 AFR AF: 0.0374

Gnomad4 AMR AF: 0.0503

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0439 Hom.: 32

Bravo AF: 0.0487

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17118382; hg19: chr14-83779178;