NM_024645.3:c.-5+20540T>C

Variant names:

• chr8-40877143-A-G
• rs2137277
• NM_024645.3:c.-5+20540T>C

Variant summary

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

The NM_024645.3(ZMAT4):​c.-5+20540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,144 control chromosomes in the GnomAD database, including 3,382 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 0.21 (3382 hom., cov: 32)
• Consequence: ZMAT4 NM_024645.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 9 publications found

Genes affected

ZMAT4 (HGNC:25844): (zinc finger matrin-type 4) Enables identical protein binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024645.3. 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
	ZMAT4	NM_024645.3	MANE Select	c.-5+20540T>C		intron	N/A	NP_078921.1
	ZMAT4	NM_001135731.2		c.-5+20540T>C		intron	N/A	NP_001129203.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMAT4	ENST00000297737.11	TSL:2 MANE Select	c.-5+20540T>C		intron	N/A	ENSP00000297737.6
	ZMAT4	ENST00000315769.11	TSL:1	c.-5+20540T>C		intron	N/A	ENSP00000319785.7
	ZMAT4	ENST00000519406.5	TSL:3	c.-5+11352T>C		intron	N/A	ENSP00000428423.1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31640 AN: 152026 Hom.: 3365 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.208 AC: 31691 AN: 152144 Hom.: 3382 Cov.: 32 AF XY: 0.207 AC XY: 15397 AN XY: 74374

African (AFR) AF: 0.235 AC: 9755 AN: 41498

American (AMR) AF: 0.245 AC: 3744 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3468

East Asian (EAS) AF: 0.0793 AC: 410 AN: 5172

South Asian (SAS) AF: 0.0972 AC: 469 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2119 AN: 10584

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13816 AN: 67994

Other (OTH) AF: 0.201 AC: 426 AN: 2116

Alfa AF: 0.214 Hom.: 1314

Bravo AF: 0.213

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.026
DANN	Benign	0.27
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2137277; hg19: chr8-40734662;