rs7528241

Variant names:

• chr1-193452230-A-C
• rs7528241
• ENST00000767304.1:n.236-5411A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-193452230-A-C
• chr1-193452230-A-G

Variant summary

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

The ENST00000767304.1(ENSG00000286285):​n.236-5411A>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: 32)
• Consequence: ENSG00000286285 ENST00000767304.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 5 publications found

Genes affected

ENSG00000286285 (HGNC:):

LINC01031 (HGNC:49017): (long intergenic non-protein coding RNA 1031)

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286285	ENST00000767304.1	n.236-5411A>C		intron_variant	Intron 2 of 3
ENSG00000286285	ENST00000767305.1	n.105-5411A>C		intron_variant	Intron 1 of 2
ENSG00000286285	ENST00000767306.1	n.62-5411A>C		intron_variant	Intron 1 of 2
LINC01031	ENST00000767397.1	n.325-5411A>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7528241; hg19: chr1-193421360;