rs7966098

Variant names:

• chr12-96044863-G-C
• rs7966098
• ENST00000824362.1:n.272-2755G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-96044863-G-C
• chr12-96044863-G-T

Variant summary

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

The ENST00000824362.1(ENSG00000307169):​n.272-2755G>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: 30)
• Consequence: ENSG00000307169 ENST00000824362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 7 publications found

Genes affected

ENSG00000307169 (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=-0.95).

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
ENSG00000307169	ENST00000824362.1	n.272-2755G>C		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824363.1	n.98-8481G>C		intron_variant	Intron 1 of 1
ENSG00000307169	ENST00000824364.1	n.143-2755G>C		intron_variant	Intron 1 of 2
ENSG00000307169	ENST00000824365.1	n.*138G>C		downstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.77
DANN	Benign	0.21
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7966098; hg19: chr12-96438641;