14-23116124-C-T

Variant names:

• chr14-23116124-C-T
• rs4982731
• ENST00000733532.1:n.234+706C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000733532.1(ENSG00000295888):​n.234+706C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,028 control chromosomes in the GnomAD database, including 35,383 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 0.68 (35383 hom., cov: 31)
• Consequence: ENSG00000295888 ENST00000733532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 29 publications found

Genes affected

ENSG00000295888 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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
ENSG00000295888	ENST00000733532.1	n.234+706C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103187 AN: 151910 Hom.: 35358 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.679 AC: 103268 AN: 152028 Hom.: 35383 Cov.: 31 AF XY: 0.676 AC XY: 50264 AN XY: 74302

African (AFR) AF: 0.609 AC: 25248 AN: 41450

American (AMR) AF: 0.657 AC: 10035 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3468

East Asian (EAS) AF: 0.842 AC: 4351 AN: 5170

South Asian (SAS) AF: 0.587 AC: 2828 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7083 AN: 10568

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49308 AN: 67972

Other (OTH) AF: 0.671 AC: 1415 AN: 2110

Alfa AF: 0.707 Hom.: 142304

Bravo AF: 0.675

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	18
DANN	Benign	0.74
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4982731; hg19: chr14-23585333;