ENST00000620266.1:n.2894G>A

Variant names:

• chr17-68129559-G-A
• rs1060021
• ENST00000620266.1:n.2894G>A

Variant summary

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

The ENST00000620266.1(ENSG00000278730):​n.2894G>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: ENSG00000278730 ENST00000620266.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 1 publications found

Genes affected

ENSG00000278730 (HGNC:):

LINC00674 (HGNC:44355): (long intergenic non-protein coding RNA 674)

LRRC37A16P (HGNC:43820): (leucine rich repeat containing 37 member A16, pseudogene)

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00674	NR_027418.1	n.4823G>A		non_coding_transcript_exon_variant	Exon 6 of 6
LRRC37A16P		n.68129559G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278730	ENST00000620266.1	n.2894G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290646	ENST00000585915.1	n.191+645C>T		intron_variant	Intron 2 of 2	5
LRRC37A16P	ENST00000586022.5	n.2107+595C>T		intron_variant	Intron 11 of 14	6

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	-0.93
CADD	Benign	6.6
DANN	Benign	0.42
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs1060021; hg19: chr17-66125700;