chr8-37598786-G-T

Variant names:

• chr8-37598786-G-T
• rs2298321
• ENST00000519691.2:n.1076C>A

Variant summary

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

The ENST00000519691.2(LINC01605):​n.1076C>A 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: 32)
• Consequence: LINC01605 ENST00000519691.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 0 publications found

Genes affected

LINC01605 (HGNC:51654): (long intergenic non-protein coding RNA 1605)

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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01605	NR_170186.1	n.779+275C>A		intron_variant	Intron 1 of 4
LINC01605	NR_170187.1	n.779+275C>A		intron_variant	Intron 1 of 6
LINC01605	NR_170188.1	n.779+275C>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01605	ENST00000519691.2	n.1076C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01605	ENST00000784554.1	n.194C>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01605	ENST00000517363.2	n.34+275C>A		intron_variant	Intron 1 of 7	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.75
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2298321; hg19: chr8-37456304;