chr10-79043121-C-T

Position:

• chr10-79043121-C-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+22626G>A 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 0.22 in 152,138 control chromosomes in the GnomAD database, including 3,763 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 0.22 (3763 hom., cov: 33)
• Consequence: ZMIZ1-AS1 NR_015429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMIZ1-AS1	NR_015429.1	n.273+22626G>A		intron_variant, non_coding_transcript_variant
ZMIZ1-AS1	NR_024429.1	n.432+5653G>A		intron_variant, non_coding_transcript_variant
ZMIZ1-AS1	NR_024431.2	n.565+5653G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMIZ1-AS1	ENST00000456353.5	n.1012+5653G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33472 AN: 152020 Hom.: 3760 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.220 AC: 33508 AN: 152138 Hom.: 3763 Cov.: 33 AF XY: 0.219 AC XY: 16273 AN XY: 74392

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.212

Alfa AF: 0.212 Hom.: 1878

Bravo AF: 0.220

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437803; hg19: chr10-80802878;