rs7807514

Variant names:

• chr7-91388581-C-G
• rs7807514
• ENST00000418395.1:n.181+72551C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-91388581-C-G
• chr7-91388581-C-T

Variant summary

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

The ENST00000418395.1(LINC02932):​n.181+72551C>G 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: LINC02932 ENST00000418395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

LINC02932 (HGNC:55875): (long intergenic non-protein coding RNA 2932)

ENSG00000235450 (HGNC:):

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02932	NR_183366.1	n.243+72551C>G		intron_variant	Intron 3 of 6
LINC02932	NR_183367.1	n.243+72551C>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02932	ENST00000418395.1	n.181+72551C>G		intron_variant	Intron 2 of 5	3
ENSG00000235450	ENST00000456952.1	n.113-7714G>C		intron_variant	Intron 1 of 1	3

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7807514; hg19: chr7-91017896;