ENST00000677024.1:n.-206A>G

Variant names:

• chr19-45692197-G-.
• NM_004597.6:c.-136C>.

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000677024.1(QPCTL):​n.-507G>. variant causes a upstream gene change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: QPCTL ENST00000677024.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: No publications found

Genes affected

SNRPD2 (HGNC:11159): (small nuclear ribonucleoprotein D2 polypeptide) The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

QPCTL (HGNC:25952): (glutaminyl-peptide cyclotransferase like) Enables glutaminyl-peptide cyclotransferase activity and zinc ion binding activity. Acts upstream of or within peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000677024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPD2	NM_004597.6		c.-136C>.		5_prime_UTR	Exon 1 of 4	NP_004588.1	P62316-1
	SNRPD2	NM_001384647.1	MANE Select	c.-309C>.		upstream_gene	N/A	NP_001371576.1	P62316-1
	SNRPD2	NM_001369751.1		c.-435C>.		upstream_gene	N/A	NP_001356680.1	P62316-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPD2	ENST00000588301.5	TSL:3	c.-136C>.		5_prime_UTR	Exon 1 of 4	ENSP00000465216.1	P62316-1
	SNRPD2	ENST00000587579.1	TSL:5	n.247C>.		non_coding_transcript_exon	Exon 2 of 2
	SNRPD2	ENST00000342669.8	TSL:1 MANE Select	c.-309C>.		upstream_gene	N/A	ENSP00000342374.2	P62316-1

Frequencies

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

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Splicing

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

Other links and lift over

hg19: chr19-46195455;