rs1439031

Positions:

• chr10-78959645-A-G
• chr10-78959645-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_015429.1(ZMIZ1-AS1):​n.641+1609T>C variant causes a intron, non coding transcript 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 NR_015429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMIZ1-AS1	NR_015429.1	n.641+1609T>C		intron_variant, non_coding_transcript_variant
ZMIZ1-AS1	NR_024429.1	n.737+1609T>C		intron_variant, non_coding_transcript_variant
ZMIZ1-AS1	NR_024431.2	n.933+1609T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMIZ1-AS1	ENST00000456353.5	n.1380+1609T>C		intron_variant, non_coding_transcript_variant		2
ZMIZ1-AS1	ENST00000428862.5	n.1353+860T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.282

Alfa AF: 0.231 Hom.: 1201

Bravo AF: 0.336

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1439031; hg19: chr10-80719402;