5-16472596-T-C

Variant names:

• chr5-16472596-T-C
• rs26015
• ENST00000747818.1:n.501-2583T>C

Variant summary

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

The ENST00000747818.1(ENSG00000289112):​n.501-2583T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,086 control chromosomes in the GnomAD database, including 46,384 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 0.78 (46384 hom., cov: 32)
• Consequence: ENSG00000289112 ENST00000747818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472
• Publications: 1 publications found

Genes affected

ENSG00000289112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747818.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289112	ENST00000747818.1		n.501-2583T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118509 AN: 151968 Hom.: 46332 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.780 AC: 118632 AN: 152086 Hom.: 46384 Cov.: 32 AF XY: 0.779 AC XY: 57919 AN XY: 74332

African (AFR) AF: 0.832 AC: 34546 AN: 41504

American (AMR) AF: 0.766 AC: 11698 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2658 AN: 3468

East Asian (EAS) AF: 0.697 AC: 3608 AN: 5174

South Asian (SAS) AF: 0.660 AC: 3182 AN: 4824

European-Finnish (FIN) AF: 0.790 AC: 8370 AN: 10594

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52010 AN: 67940

Other (OTH) AF: 0.778 AC: 1640 AN: 2108

Alfa AF: 0.777 Hom.: 7767

Bravo AF: 0.782

Asia WGS AF: 0.731 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.53
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs26015; hg19: chr5-16472705;