chr7-77010554-T-A

Position:

• chr7-77010554-T-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000579700.1(DTX2P1-UPK3BP1-PMS2P11):​n.815+4779T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 16)
• Consequence: DTX2P1-UPK3BP1-PMS2P11 ENST00000579700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

DTX2P1-UPK3BP1-PMS2P11 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTX2P1-UPK3BP1-PMS2P11	NR_023383.1	n.1096-1326T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTX2P1-UPK3BP1-PMS2P11	ENST00000579700.1	n.815+4779T>A		intron_variant		2
DTX2P1-UPK3BP1-PMS2P11	ENST00000584900.5	n.969-1326T>A		intron_variant		2
DTX2P1-UPK3BP1-PMS2P11	ENST00000636308.1	n.2007-1326T>A		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 16

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6955651; hg19: chr7-76639871;