rs4674024

Variant names:

• chr2-215766643-C-G
• rs4674024
• ENST00000413563.6:n.17-16226G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-215766643-C-G
• chr2-215766643-C-T

Variant summary

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

The ENST00000413563.6(LINC00607):​n.17-16226G>C 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: LINC00607 ENST00000413563.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 5 publications found

Genes affected

LINC00607 (HGNC:43944): (long intergenic non-protein coding RNA 607)

ENSG00000288791 (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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00607	NR_037195.1	n.212-16226G>C		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00607	ENST00000413563.6	n.17-16226G>C		intron_variant	Intron 1 of 3	4
LINC00607	ENST00000417922.2	n.144-16226G>C		intron_variant	Intron 1 of 5	4
LINC00607	ENST00000423530.5	n.285-19249G>C		intron_variant	Intron 2 of 8	2

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	1.2
DANN	Benign	0.35
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4674024; hg19: chr2-216631366;