rs12155172

Variant names:

• chr7-20954872-A-C
• rs12155172
• ENST00000447262.2:n.152-65996A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-20954872-A-C
• chr7-20954872-A-G
• chr7-20954872-A-T

Variant summary

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

The ENST00000447262.2(LINC01162):​n.152-65996A>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: 31)
• Consequence: LINC01162 ENST00000447262.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 64 publications found

Genes affected

LINC01162 (HGNC:49528): (long intergenic non-protein coding RNA 1162)

ENSG00000285592 (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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01162	NR_126381.1	n.152-65996A>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01162	ENST00000447262.2	n.152-65996A>C		intron_variant	Intron 2 of 5	5
LINC01162	ENST00000661032.1	n.207-5808A>C		intron_variant	Intron 2 of 8
LINC01162	ENST00000742942.1	n.257-5808A>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 191253

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.48
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs12155172; hg19: chr7-20994491;