5-32831564-T-C

Variant names:

• chr5-32831564-T-C
• rs13154066
• ENST00000841800.1:n.496-20469A>G

Variant summary

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

The ENST00000841800.1(ENSG00000250697):​n.496-20469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,010 control chromosomes in the GnomAD database, including 27,306 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 0.60 (27306 hom., cov: 31)
• Consequence: ENSG00000250697 ENST00000841800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 15 publications found

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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
ENSG00000250697	ENST00000841800.1	n.496-20469A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90892 AN: 151892 Hom.: 27274 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.599 AC: 90979 AN: 152010 Hom.: 27306 Cov.: 31 AF XY: 0.599 AC XY: 44468 AN XY: 74284

African (AFR) AF: 0.609 AC: 25242 AN: 41450

American (AMR) AF: 0.584 AC: 8924 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3347 AN: 5158

South Asian (SAS) AF: 0.582 AC: 2796 AN: 4806

European-Finnish (FIN) AF: 0.591 AC: 6259 AN: 10586

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40393 AN: 67946

Other (OTH) AF: 0.612 AC: 1294 AN: 2114

Alfa AF: 0.592 Hom.: 81028

Bravo AF: 0.598

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs13154066; hg19: chr5-32831670;