8-64817650-G-T

Variant names:

• chr8-64817650-G-T
• rs6472155
• ENST00000833569.1:n.685G>T

Variant summary

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

The ENST00000833569.1(ENSG00000287998):​n.685G>T 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: 31)
• Consequence: ENSG00000287998 ENST00000833569.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 14 publications found

Genes affected

ENSG00000287998 (HGNC:):

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375878	NR_188109.1	n.-47C>A		upstream_gene_variant
LOC105375878	NR_188110.1	n.-47C>A		upstream_gene_variant
LOC105375878	NR_188111.1	n.-47C>A		upstream_gene_variant
LOC105375879	XR_928992.3	n.*218G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287998	ENST00000833569.1	n.685G>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287998	ENST00000665380.1	n.367+13739G>T		intron_variant	Intron 2 of 2
ENSG00000287998	ENST00000833561.1	n.356+13739G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs6472155; hg19: chr8-65730207;