5-32888712-C-T

Variant names:

• chr5-32888712-C-T
• rs10472828
• ENST00000666525.1:n.674G>A

Variant summary

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

The ENST00000666525.1(ENSG00000250697):​n.674G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,922 control chromosomes in the GnomAD database, including 13,365 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 0.41 (13365 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000666525.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 19 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666525.1. 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
	ENSG00000250697	ENST00000666525.1		n.674G>A		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000250697	ENST00000841800.1		n.495+941G>A		intron	N/A
	ENSG00000309532	ENST00000841854.1		n.583-1041C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61780 AN: 151804 Hom.: 13358 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.407 AC: 61803 AN: 151922 Hom.: 13365 Cov.: 32 AF XY: 0.408 AC XY: 30286 AN XY: 74242

African (AFR) AF: 0.260 AC: 10778 AN: 41460

American (AMR) AF: 0.508 AC: 7747 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2875 AN: 5162

South Asian (SAS) AF: 0.518 AC: 2491 AN: 4810

European-Finnish (FIN) AF: 0.389 AC: 4105 AN: 10550

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31072 AN: 67918

Other (OTH) AF: 0.406 AC: 858 AN: 2112

Alfa AF: 0.444 Hom.: 47192

Bravo AF: 0.409

Asia WGS AF: 0.509 AC: 1770 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.48
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10472828; hg19: chr5-32888818;