rs17277375

Variant names:

• chr14-20441313-C-T
• rs17277375
• ENST00000687238.1:n.832+283C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687238.1(ENSG00000291038):​n.832+283C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,118 control chromosomes in the GnomAD database, including 9,248 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 0.35 (9248 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000291038 ENST00000687238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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
ENSG00000291038	ENST00000687238.1	n.832+283C>T		intron_variant	Intron 5 of 7
ENSG00000291038	ENST00000700970.1	n.610+541C>T		intron_variant	Intron 3 of 4
ENSG00000259162	ENST00000553568.1	n.*45C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52509 AN: 152000 Hom.: 9250 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.345 AC: 52531 AN: 152116 Hom.: 9248 Cov.: 33 AF XY: 0.350 AC XY: 26010 AN XY: 74370

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.373

Alfa AF: 0.353 Hom.: 13140

Bravo AF: 0.328

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17277375; hg19: chr14-20909472;