chr10-78959645-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428862.5(ZMIZ1-AS1):​n.1353+860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,982 control chromosomes in the GnomAD database, including 10,491 homozygotes. 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: 𝑓 0.33 (10491 hom., cov: 32)
• Consequence: ZMIZ1-AS1 ENST00000428862.5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000428862.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMIZ1-AS1	NR_015429.1		n.641+1609T>C		intron	N/A
	ZMIZ1-AS1	NR_024429.1		n.737+1609T>C		intron	N/A
	ZMIZ1-AS1	NR_024431.2		n.933+1609T>C		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49690 AN: 151864 Hom.: 10455 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.328 AC: 49788 AN: 151982 Hom.: 10491 Cov.: 32 AF XY: 0.331 AC XY: 24570 AN XY: 74284

African (AFR) AF: 0.583 AC: 24167 AN: 41424

American (AMR) AF: 0.243 AC: 3719 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3466

East Asian (EAS) AF: 0.547 AC: 2813 AN: 5140

South Asian (SAS) AF: 0.443 AC: 2132 AN: 4810

European-Finnish (FIN) AF: 0.233 AC: 2456 AN: 10558

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12998 AN: 67990

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.285 Hom.: 5603

Bravo AF: 0.336

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.70
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;