rs6790925

Variant names:

• chr3-30438593-C-G
• rs6790925
• ENST00000691186.2:n.282-30440C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-30438593-C-G
• chr3-30438593-C-T

Variant summary

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

The ENST00000691186.2(ENSG00000289450):​n.282-30440C>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: ENSG00000289450 ENST00000691186.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 18 publications found

Genes affected

ENSG00000289450 (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=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_001740627.2	n.213-30440C>G		intron_variant	Intron 3 of 3
LOC101927995	XR_001740628.2	n.261-30440C>G		intron_variant	Intron 4 of 4
LOC101927995	XR_007095856.1	n.257-30440C>G		intron_variant	Intron 4 of 4
LOC105377013	XR_940683.2	n.293+2414G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289450	ENST00000691186.2	n.282-30440C>G		intron_variant	Intron 3 of 3
ENSG00000227549	ENST00000813769.1	n.399-16227G>C		intron_variant	Intron 4 of 5
ENSG00000289450	ENST00000813894.1	n.392-30440C>G		intron_variant	Intron 3 of 3
ENSG00000289450	ENST00000813895.1	n.225-30440C>G		intron_variant	Intron 3 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.: 19117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.053
DANN	Benign	0.49
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs6790925; hg19: chr3-30480085;