rs6955651

Variant names:

• chr7-77010554-T-A
• rs6955651
• ENST00000579700.2:n.815+4779T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-77010554-T-A
• chr7-77010554-T-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000579700.2(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 ENST00000579700.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 12 publications found

Genes affected

DTX2P1-UPK3BP1-PMS2P11 (HGNC:42360): (DTX2P1-UPK3BP1-PMS2P11 readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription spanning multiple pseudogenes: DTX2P1 (DTX2 pseudogene 1), UPK3BP1 (uroplakin 3B pseudogene 1), PMS2P11 (PMS1 homolog 2, mismatch repair system component pseudogene 11). Some transcripts may also extend to PMS2P9 (PMS1 homolog 2, mismatch repair system component pseudogene 9). The readthrough transcripts likely do not encode functional proteins. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DTX2P1-UPK3BP1-PMS2P11	NR_023383.1	n.1096-1326T>A		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DTX2P1-UPK3BP1-PMS2P11	ENST00000579700.2	n.815+4779T>A		intron_variant	Intron 6 of 10	2
DTX2P1-UPK3BP1-PMS2P11	ENST00000584900.5	n.969-1326T>A		intron_variant	Intron 6 of 10	2
DTX2P1-UPK3BP1-PMS2P11	ENST00000636308.1	n.2007-1326T>A		intron_variant	Intron 10 of 14	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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6955651; hg19: chr7-76639871;