10-58503165-C-G

Variant names:

• chr10-58503165-C-G
• rs1427209
• ENST00000720299.1:n.561C>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.561C>G variant causes a non coding transcript exon 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: ENSG00000293977 ENST00000720299.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 4 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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.547C>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105378316	XR_945981.3	n.874C>G		non_coding_transcript_exon_variant	Exon 6 of 6
LOC105378316	XR_945982.3	n.840C>G		non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293977	ENST00000720299.1	n.561C>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000293977	ENST00000720300.1	n.126C>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000293977	ENST00000720301.1	n.473C>G		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000293977	ENST00000720302.1	n.610C>G		non_coding_transcript_exon_variant	Exon 2 of 2

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	-0.85
CADD	Benign	0.41
DANN	Benign	0.77
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1427209; hg19: chr10-60262925;