ENST00000838110.1:n.269-27708G>A

Variant names:

• chr10-78862599-C-T
• rs570677
• ENST00000838110.1:n.269-27708G>A

Variant summary

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

The ENST00000838110.1(ZMIZ1-AS1):​n.269-27708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,174 control chromosomes in the GnomAD database, including 18,208 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 0.43 (18208 hom., cov: 33)
• Consequence: ZMIZ1-AS1 ENST00000838110.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838110.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMIZ1-AS1	ENST00000838110.1		n.269-27708G>A		intron	N/A
	ZMIZ1-AS1	ENST00000838111.1		n.421-27708G>A		intron	N/A
	ZMIZ1-AS1	ENST00000838112.1		n.334+8715G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64846 AN: 152056 Hom.: 18148 Cov.: 33

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.427 AC: 64968 AN: 152174 Hom.: 18208 Cov.: 33 AF XY: 0.429 AC XY: 31900 AN XY: 74388

African (AFR) AF: 0.782 AC: 32503 AN: 41544

American (AMR) AF: 0.332 AC: 5071 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3353 AN: 5182

South Asian (SAS) AF: 0.549 AC: 2647 AN: 4818

European-Finnish (FIN) AF: 0.276 AC: 2916 AN: 10576

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16379 AN: 67982

Other (OTH) AF: 0.374 AC: 791 AN: 2114

Alfa AF: 0.302 Hom.: 13888

Bravo AF: 0.443

Asia WGS AF: 0.595 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs570677; hg19: chr10-80622356;