10-58484957-T-G

Variant names:

• chr10-58484957-T-G
• rs7096154
• ENST00000720299.1:n.533-18180T>G

Variant summary

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

The ENST00000720299.1(ENSG00000293977):​n.533-18180T>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: 30)
• Consequence: ENSG00000293977 ENST00000720299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 3 publications found

Genes affected

ENSG00000293977 (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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.518+17275T>G		intron_variant	Intron 3 of 3
LOC105378316	XR_945981.3	n.845+3473T>G		intron_variant	Intron 5 of 5
LOC105378316	XR_945982.3	n.811+3473T>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293977	ENST00000720299.1	n.533-18180T>G		intron_variant	Intron 1 of 1
ENSG00000293977	ENST00000720300.1	n.98-18180T>G		intron_variant	Intron 1 of 1
ENSG00000293977	ENST00000720301.1	n.444+17275T>G		intron_variant	Intron 3 of 3
ENSG00000293977	ENST00000720302.1	n.581+17275T>G		intron_variant	Intron 1 of 1

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	-0.88
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7096154; hg19: chr10-60244717;