rs17118382

Variant names:

• chr14-83312834-T-C
• rs17118382

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 0.0492 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0374 AC: 1553 AN: 41568

American (AMR) AF: 0.0503 AC: 769 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1258 AN: 5166

South Asian (SAS) AF: 0.0400 AC: 193 AN: 4820

European-Finnish (FIN) AF: 0.0542 AC: 576 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2993 AN: 68004

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0436 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
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs17118382; hg19: chr14-83779178;