chr4-173957277-C-T

Variant names:

• chr4-173957277-C-T
• rs10588631
• ENST00000511291.1:n.146-29287G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000511291.1(ENSG00000251216):​n.146-29287G>A 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: 21)
• Consequence: ENSG00000251216 ENST00000511291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13

Genes affected

ENSG00000251216 (HGNC:):

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377543	NR_188466.1	n.365-19914G>A		intron_variant	Intron 2 of 3
LOC105377543	NR_188467.1	n.261-19914G>A		intron_variant	Intron 1 of 2
LOC105377543	NR_188468.1	n.261-19914G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251216	ENST00000511291.1	n.146-29287G>A		intron_variant	Intron 1 of 2	3
LINC02269	ENST00000656853.1	n.641+1228C>T		intron_variant	Intron 4 of 4
ENSG00000251216	ENST00000662648.1	n.423-19914G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 21

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

GnomAD4 genome Cov.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10588631; hg19: chr4-174878428;