ENST00000671572.2:n.89+2257G>T

Variant names:

• chr6-70378113-G-T
• rs10498873
• ENST00000671572.2:n.89+2257G>T

Variant summary

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

The ENST00000671572.2(LINC01610):​n.89+2257G>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: 29)
• Consequence: LINC01610 ENST00000671572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 3 publications found

Genes affected

LINC01610 (HGNC:51676): (long intergenic non-protein coding RNA 1610)

ENSG00000310357 (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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377848	XR_942670.2	n.141+3194C>A		intron_variant	Intron 1 of 3
LOC105377848	XR_942673.1	n.141+3194C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01610	ENST00000671572.2	n.89+2257G>T		intron_variant	Intron 1 of 6
ENSG00000310357	ENST00000849277.1	n.925+3194C>A		intron_variant	Intron 5 of 5
ENSG00000310357	ENST00000849278.1	n.490+3194C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs10498873; hg19: chr6-71087816;