4-151891966-G-C

Variant names:

• chr4-151891966-G-C
• rs4696302
• ENST00000716626.1:n.154-637C>G

Variant summary

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

The ENST00000716626.1(ENSG00000249818):​n.154-637C>G 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: 33)
• Consequence: ENSG00000249818 ENST00000716626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 3 publications found

Genes affected

ENSG00000249818 (HGNC:):

LINC03074 (HGNC:56654): (long intergenic non-protein coding RNA 3074)

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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC127898557	NR_183042.1	n.383-29798G>C		intron_variant	Intron 2 of 3
LOC102724700	NR_188364.1	n.264-637C>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249818	ENST00000716626.1	n.154-637C>G		intron_variant	Intron 1 of 2
ENSG00000249818	ENST00000716627.1	n.275-637C>G		intron_variant	Intron 2 of 4
LINC03074	ENST00000731483.1	n.377-29798G>C		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.47
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4696302; hg19: chr4-152813118;