22-29736799-T-G

Position:

• chr22-29736799-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001003692.2(ZMAT5):​c.383+1531A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.00027 (0 hom., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ZMAT5 NM_001003692.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.65

Genes affected

ZMAT5 (HGNC:28046): (zinc finger matrin-type 5) Predicted to enable zinc ion binding activity. Predicted to be involved in RNA splicing. Located in nucleoplasm. Part of U12-type spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZMAT5	NM_001003692.2	c.383+1531A>C		intron_variant		ENST00000344318.4	NP_001003692.1
ZMAT5	NM_001318129.2	c.383+1531A>C		intron_variant			NP_001305058.1
ZMAT5	NM_019103.3	c.383+1531A>C		intron_variant			NP_061976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZMAT5	ENST00000344318.4	c.383+1531A>C		intron_variant		1	NM_001003692.2	ENSP00000344241.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 35 AN: 129046 Hom.: 0 Cov.: 22 FAILED QC

Gnomad AFR AF: 0.000583

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000334

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000581

Gnomad FIN AF: 0.000664

Gnomad MID AF: 0.00476

Gnomad NFE AF: 0.0000490

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000271 AC: 35 AN: 129046 Hom.: 0 Cov.: 22 AF XY: 0.000372 AC XY: 23 AN XY: 61750

Gnomad4 AFR AF: 0.000583

Gnomad4 AMR AF: 0.000334

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000581

Gnomad4 FIN AF: 0.000664

Gnomad4 NFE AF: 0.0000490

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.014
DANN	Benign	0.087

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs131259; hg19: chr22-30132788;