chr10-78959645-A-T

Variant names:

• chr10-78959645-A-T
• rs1439031
• ENST00000428862.5:n.1353+860T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000456353.5(ZMIZ1-AS1):​n.1380+1609T>A variant causes a intron 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: ZMIZ1-AS1 ENST00000456353.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 1 publications found

Genes affected

ZMIZ1-AS1 (HGNC:27433): (ZMIZ1 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456353.5. 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
	ZMIZ1-AS1	NR_015429.1		n.641+1609T>A		intron	N/A
	ZMIZ1-AS1	NR_024429.1		n.737+1609T>A		intron	N/A
	ZMIZ1-AS1	NR_024431.2		n.933+1609T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMIZ1-AS1	ENST00000428862.5	TSL:5	n.1353+860T>A		intron	N/A
	ZMIZ1-AS1	ENST00000456353.5	TSL:2	n.1380+1609T>A		intron	N/A
	ZMIZ1-AS1	ENST00000838110.1		n.113-33156T>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1439031; hg19: chr10-80719402;