5-114513597-C-T

Variant names:

• chr5-114513597-C-T
• rs400028
• ENST00000514115.6:n.332-17419G>A

Variant summary

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

The ENST00000514115.6(ENSG00000246316):​n.332-17419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 151,842 control chromosomes in the GnomAD database, including 41,838 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 0.74 (41838 hom., cov: 31)
• Consequence: ENSG00000246316 ENST00000514115.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 3 publications found

Genes affected

ENSG00000246316 (HGNC:59115):

LOC101927078 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514115.6. 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
	LOC101927078	NR_130785.1		n.343-17419G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246316	ENST00000514115.6	TSL:3	n.332-17419G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112632 AN: 151724 Hom.: 41796 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.742 AC: 112729 AN: 151842 Hom.: 41838 Cov.: 31 AF XY: 0.746 AC XY: 55318 AN XY: 74184

African (AFR) AF: 0.741 AC: 30655 AN: 41356

American (AMR) AF: 0.821 AC: 12542 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2654 AN: 3468

East Asian (EAS) AF: 0.820 AC: 4224 AN: 5154

South Asian (SAS) AF: 0.719 AC: 3459 AN: 4810

European-Finnish (FIN) AF: 0.731 AC: 7678 AN: 10502

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49060 AN: 67970

Other (OTH) AF: 0.753 AC: 1588 AN: 2110

Alfa AF: 0.731 Hom.: 96989

Bravo AF: 0.751

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.22

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: rs400028;

hg19: chr5-113849294;