ENST00000523257.1:n.502G>A

Variant names:

• chr8-23483033-C-T
• rs6557675
• ENST00000523257.1:n.502G>A

Variant summary

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

The ENST00000523257.1(ENSG00000253483):​n.502G>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 0.347 in 435,386 control chromosomes in the GnomAD database, including 28,236 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 0.38 (11942 hom., cov: 33)
  • Exomes 𝑓: 0.33 (16294 hom.)
• Consequence: ENSG00000253483 ENST00000523257.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 12 publications found

Genes affected

ENSG00000253483 (HGNC:):

ENTPD4-DT (HGNC:55536): (ENTPD4 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD4-DT	NR_186531.1	n.5414C>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENTPD4-DT	NR_186532.1	n.5414C>T		non_coding_transcript_exon_variant	Exon 2 of 3
ENTPD4-DT	NR_186533.1	n.4190C>T		non_coding_transcript_exon_variant	Exon 3 of 5
LOC646708		n.23483033C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253483	ENST00000523257.1	n.502G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENTPD4-DT	ENST00000521021.1	n.492-1800C>T		intron_variant	Intron 1 of 1	2
ENSG00000287166	ENST00000806162.1	n.-61C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57909 AN: 151912 Hom.: 11929 Cov.: 33

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.371

GnomAD4 exome AF: 0.329 AC: 93135 AN: 283360 Hom.: 16294 Cov.: 0 AF XY: 0.328 AC XY: 51153 AN XY: 156004

African (AFR) AF: 0.537 AC: 4334 AN: 8072

American (AMR) AF: 0.506 AC: 9207 AN: 18202

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 2334 AN: 7460

East Asian (EAS) AF: 0.284 AC: 3699 AN: 13010

South Asian (SAS) AF: 0.359 AC: 16685 AN: 46452

European-Finnish (FIN) AF: 0.295 AC: 4428 AN: 15008

Middle Eastern (MID) AF: 0.336 AC: 395 AN: 1174

European-Non Finnish (NFE) AF: 0.296 AC: 47118 AN: 159270

Other (OTH) AF: 0.335 AC: 4935 AN: 14712

GnomAD4 genome AF: 0.381 AC: 57974 AN: 152026 Hom.: 11942 Cov.: 33 AF XY: 0.381 AC XY: 28325 AN XY: 74320

African (AFR) AF: 0.531 AC: 21990 AN: 41388

American (AMR) AF: 0.441 AC: 6738 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.294 AC: 1517 AN: 5160

South Asian (SAS) AF: 0.365 AC: 1761 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3322 AN: 10588

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20529 AN: 67994

Other (OTH) AF: 0.373 AC: 786 AN: 2110

Alfa AF: 0.333 Hom.: 27996

Bravo AF: 0.400

Asia WGS AF: 0.334 AC: 1161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.87
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs6557675; hg19: chr8-23340546;