chr8-23483033-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000523257.1(ENSG00000253483):​n.502G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: ENSG00000253483 ENST00000523257.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 0 publications found

Genes affected

ENSG00000253483 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523257.1. 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
	ENTPD4-DT	NR_186531.1		n.5414C>G		non_coding_transcript_exon	Exon 2 of 4
	ENTPD4-DT	NR_186532.1		n.5414C>G		non_coding_transcript_exon	Exon 2 of 3
	ENTPD4-DT	NR_186533.1		n.4190C>G		non_coding_transcript_exon	Exon 3 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253483	ENST00000523257.1	TSL:6	n.502G>C		non_coding_transcript_exon	Exon 1 of 1
	ENTPD4-DT	ENST00000521021.1	TSL:2	n.492-1800C>G		intron	N/A
	ENSG00000287166	ENST00000806162.1		n.-61C>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.099
DANN	Benign	0.69
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;