rs17427680

Variant names:

• chr14-30340938-T-G
• rs17427680

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 0.0405 in 152,308 control chromosomes in the GnomAD database, including 147 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 0.041 (147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0598 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: 0.0406 AC: 6175 AN: 152190 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0405 AC: 6175 AN: 152308 Hom.: 147 Cov.: 32 AF XY: 0.0413 AC XY: 3074 AN XY: 74478

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0331

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0588

Gnomad4 NFE AF: 0.0614

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0477 Hom.: 54

Bravo AF: 0.0360

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17427680; hg19: chr14-30810144;