7-77000309-G-C

Position:

• chr7-77000309-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000579700.1(DTX2P1-UPK3BP1-PMS2P11):​n.261G>C variant causes a splice region, 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: DTX2P1-UPK3BP1-PMS2P11 ENST00000579700.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

Genes affected

DTX2P1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTX2P1-UPK3BP1-PMS2P11	NR_023383.1	n.541G>C		splice_region_variant, non_coding_transcript_exon_variant	3/11
DTX2P1		n.77000309G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTX2P1	ENST00000425797.2	n.1143G>C		splice_region_variant, non_coding_transcript_exon_variant	5/8	6
DTX2P1-UPK3BP1-PMS2P11	ENST00000579700.1	n.261G>C		splice_region_variant, non_coding_transcript_exon_variant	3/9	2
DTX2P1-UPK3BP1-PMS2P11	ENST00000584900.5	n.414G>C		splice_region_variant, non_coding_transcript_exon_variant	3/11	2
DTX2P1-UPK3BP1-PMS2P11	ENST00000636308.1	n.1371G>C		splice_region_variant, non_coding_transcript_exon_variant	6/15	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 15

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1638152; hg19: chr7-76629626;