rs6557675

chr8-23483033-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000523257.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523257.1	n.502G>A		non_coding_transcript_exon_variant	1/1
ENTPD4-DT	ENST00000521021.1	n.492-1800C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR exome AF: 0.537

Gnomad4 AMR exome AF: 0.506

Gnomad4 ASJ exome AF: 0.313

Gnomad4 EAS exome AF: 0.284

Gnomad4 SAS exome AF: 0.359

Gnomad4 FIN exome AF: 0.295

Gnomad4 NFE exome AF: 0.296

Gnomad4 OTH exome AF: 0.335

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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.373

Alfa AF: 0.319 Hom.: 16357

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6557675; hg19: chr8-23340546;