8-88572819-G-T

Variant names:

• chr8-88572819-G-T
• rs7838490
• ENST00000518631.1:n.214+29989G>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000518631.1(ENSG00000253553):​n.214+29989G>T variant causes a intron 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: 32)
• Consequence: ENSG00000253553 ENST00000518631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

ENSG00000253553 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -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
LOC105375629	XR_001745651.3	n.85-6707C>A		intron_variant	Intron 1 of 6
LOC105375630	XR_001745653.3	n.355+30009G>T		intron_variant	Intron 3 of 7
LOC105375630	XR_007060998.1	n.330+29989G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253553	ENST00000518631.1	n.214+29989G>T		intron_variant	Intron 1 of 1	4
ENSG00000253553	ENST00000520312.1	n.156+30060G>T		intron_variant	Intron 1 of 1	4
ENSG00000253553	ENST00000521433.1	n.310+30009G>T		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7838490; hg19: chr8-89585048;