rs17111750

Variant names:

• chr14-20442249-C-T
• rs17111750
• ENST00000687238.1:n.915+141C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687238.1(ENSG00000291038):​n.915+141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,978 control chromosomes in the GnomAD database, including 7,034 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 0.30 (7034 hom., cov: 32)
• Consequence: ENSG00000291038 ENST00000687238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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.915+141C>T		intron	N/A
	ENSG00000291038	ENST00000700970.2		n.693+141C>T		intron	N/A
	ENSG00000291038	ENST00000800199.1		n.841+141C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45536 AN: 151860 Hom.: 7029 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.300 AC: 45570 AN: 151978 Hom.: 7034 Cov.: 32 AF XY: 0.302 AC XY: 22423 AN XY: 74264

African (AFR) AF: 0.278 AC: 11507 AN: 41450

American (AMR) AF: 0.242 AC: 3694 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1406 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5166

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3779 AN: 10528

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21222 AN: 67962

Other (OTH) AF: 0.319 AC: 672 AN: 2108

Alfa AF: 0.305 Hom.: 12224

Bravo AF: 0.289

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.64
PhyloP100		0.0090

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: rs17111750;

hg19: chr14-20910408;