rs1370562

chr10-79065692-G-Achr10-79065692-G-Cchr10-79065692-G-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.273+55C>T 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 0.24 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 NR_015429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMIZ1-AS1	NR_015429.1	n.273+55C>T		intron_variant, non_coding_transcript_variant
ZMIZ1-AS1	NR_024429.1	n.273+55C>T		intron_variant, non_coding_transcript_variant
ZMIZ1-AS1	NR_024431.2	n.273+55C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMIZ1-AS1	ENST00000456353.5	n.720+55C>T		intron_variant, non_coding_transcript_variant		2
ZMIZ1-AS1	ENST00000440151.3	n.171+55C>T		intron_variant, non_coding_transcript_variant		3
ZMIZ1-AS1	ENST00000665190.1	n.106+55C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.179

Gnomad4 OTH exome AF: 0.250

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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.227

Alfa AF: 0.212 Hom.: 5291

Bravo AF: 0.235

Asia WGS AF: 0.366 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370562; hg19: chr10-80825449;