2-240582850-A-G

Variant names:

• chr2-240582850-A-G
• rs1133353
• ENST00000567819.1:n.3850T>C

Variant summary

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

The ENST00000567819.1(CAPN10-DT):​n.3850T>C 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: 34)
• Consequence: CAPN10-DT ENST00000567819.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33
• Publications: 10 publications found

Genes affected

CAPN10-DT (HGNC:48839): (CAPN10 divergent transcript)

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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAPN10-DT	NR_103792.1	n.3467T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN10-DT	ENST00000567819.1	n.3850T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
CAPN10-DT	ENST00000791520.1	n.709T>C		non_coding_transcript_exon_variant	Exon 3 of 3
CAPN10-DT	ENST00000791521.1	n.242T>C		non_coding_transcript_exon_variant	Exon 2 of 2
CAPN10-DT	ENST00000791519.1	n.376-1175T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.74
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1133353; hg19: chr2-241522267;