rs17277375

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

ENSG00000291038 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687238.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291038	ENST00000687238.1		n.832+283C>T		intron	N/A
	ENSG00000291038	ENST00000700970.2		n.610+541C>T		intron	N/A
	ENSG00000291038	ENST00000800199.1		n.758+541C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.324 AC: 13436 AN: 41468

American (AMR) AF: 0.263 AC: 4021 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1559 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1907 AN: 5176

South Asian (SAS) AF: 0.486 AC: 2343 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4513 AN: 10586

Middle Eastern (MID) AF: 0.445 AC: 129 AN: 290

European-Non Finnish (NFE) AF: 0.345 AC: 23469 AN: 67984

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.350 Hom.: 16188

Bravo AF: 0.328

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.47
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17277375;

hg19: chr14-20909472;