10-79065692-G-A

Variant names:

• chr10-79065692-G-A
• rs1370562
• ENST00000440151.3:n.171+55C>T

Variant summary

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

The ENST00000440151.3(ZMIZ1-AS1):​n.171+55C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,068 control chromosomes in the GnomAD database, including 4,680 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 0.24 (4679 hom., cov: 32)
  • Exomes 𝑓: 0.26 (1 hom.)
• Consequence: ZMIZ1-AS1 ENST00000440151.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440151.3. 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.273+55C>T		intron	N/A
	ZMIZ1-AS1	NR_024429.1		n.273+55C>T		intron	N/A
	ZMIZ1-AS1	NR_024431.2		n.273+55C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMIZ1-AS1	ENST00000440151.3	TSL:3	n.171+55C>T		intron	N/A
	ZMIZ1-AS1	ENST00000456353.5	TSL:2	n.720+55C>T		intron	N/A
	ZMIZ1-AS1	ENST00000665190.1		n.106+55C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36524 AN: 151908 Hom.: 4679 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.229

GnomAD4 exome AF: 0.262 AC: 11 AN: 42 Hom.: 1 AF XY: 0.182 AC XY: 4 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.625 AC: 5 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.179 AC: 5 AN: 28

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.240 AC: 36543 AN: 152026 Hom.: 4679 Cov.: 32 AF XY: 0.249 AC XY: 18505 AN XY: 74308

African (AFR) AF: 0.234 AC: 9691 AN: 41444

American (AMR) AF: 0.286 AC: 4371 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2293 AN: 5160

South Asian (SAS) AF: 0.332 AC: 1599 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3496 AN: 10560

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13823 AN: 67972

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.213 Hom.: 7366

Bravo AF: 0.235

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs1370562; hg19: chr10-80825449;