4-173957277-C-G

Variant names:

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

Variant summary

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

The ENST00000511291.1(ENSG00000251216):​n.146-29287G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000753 in 132,842 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 𝑓 0.0000075 (0 hom., cov: 21)
• Consequence: ENSG00000251216 ENST00000511291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13
• Publications: 0 publications found

Genes affected

ENSG00000251216 (HGNC:):

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

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=-1.09).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511291.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105377543	NR_188466.1		n.365-19914G>C		intron	N/A
	LOC105377543	NR_188467.1		n.261-19914G>C		intron	N/A
	LOC105377543	NR_188468.1		n.261-19914G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251216	ENST00000511291.1	TSL:3	n.146-29287G>C		intron	N/A
	LINC02269	ENST00000656853.1		n.641+1228C>G		intron	N/A
	ENSG00000251216	ENST00000662648.2		n.423-19914G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000753 AC: 1 AN: 132842 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000156

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000753 AC: 1 AN: 132842 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 64550

African (AFR) AF: 0.00 AC: 0 AN: 32148

American (AMR) AF: 0.00 AC: 0 AN: 13204

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3266

East Asian (EAS) AF: 0.00 AC: 0 AN: 4658

South Asian (SAS) AF: 0.00 AC: 0 AN: 3796

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8834

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 302

European-Non Finnish (NFE) AF: 0.0000156 AC: 1 AN: 63972

Other (OTH) AF: 0.00 AC: 0 AN: 1868

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.15
PhyloP100		-7.1

Splicing

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

Other links and lift over

dbSNP: rs10588631; hg19: chr4-174878428;