rs10635793

Variant names:

• chr4-80191461-CTATAT-C
• rs10635793
• ENST00000339711.8:c.-982-10_-982-6delTATAT

Your query was ambiguous. Multiple possible variants found:

• chr4-80191461-CTATAT-C
• chr4-80191461-CTATAT-CTATATTATAT

Variant summary

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

The NM_020226.4(PRDM8):​c.-982-8_-982-4delTATTA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: PRDM8 NM_020226.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609
• Publications: 0 publications found

Genes affected

PRDM8 (HGNC:13993): (PR/SET domain 8) This gene encodes a protein that belongs to a conserved family of histone methyltransferases that predominantly act as negative regulators of transcription. The encoded protein contains an N-terminal Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain and a double zinc-finger domain. Knockout of this gene in mouse results in mistargeting by neurons of the dorsal telencephalon, abnormal itch-like behavior, and impaired differentiation of rod bipolar cells. In humans, the protein has been shown to interact with the phosphatase laforin and the ubiquitin ligase malin, which regulate glycogen construction in the cytoplasm. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

PRDM8-AS1 (HGNC:55581): (PRDM8 antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020226.4. 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
	PRDM8	NM_020226.4		c.-982-8_-982-4delTATTA		splice_region intron	N/A	NP_064611.3
	PRDM8-AS1	NR_183911.1		n.486+740_486+744delATATA		intron	N/A
	PRDM8-AS1	NR_183912.1		n.486+740_486+744delATATA		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRDM8	ENST00000339711.8	TSL:1	c.-982-10_-982-6delTATAT		splice_region intron	N/A	ENSP00000339764.4	Q9NQV8-1
	PRDM8	ENST00000515013.5	TSL:1	c.-982-10_-982-6delTATAT		splice_region intron	N/A	ENSP00000425149.1	E9PEH0
	PRDM8	ENST00000504452.5	TSL:5	c.-772-2651_-772-2647delTATAT		intron	N/A	ENSP00000423985.1	Q9NQV8-1

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs10635793; hg19: chr4-81112615;