Genetic Variant ZMYM4:c.86-7823A>G (chr1-35351102-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005095.3(ZMYM4):c.86-7823A>G variant causes a intron change. The variant allele was found at a frequency of 0.0693 in 882,752 control chromosomes in the GnomAD database, including 7,870 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 0.069 ( 970 hom., cov: 32)

Exomes 𝑓: 0.069 ( 6900 hom. )

Consequence

ZMYM4
NM_005095.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.39

Publications

3 publications found

Variant links:

Genes affected

ZMYM4 (HGNC:13055): (zinc finger MYM-type containing 4) Predicted to enable DNA binding activity. Involved in cytoskeleton organization and regulation of cell morphogenesis. [provided by Alliance of Genome Resources, Apr 2022]

ZMYM4 links:

RPL5P4 (HGNC:36095): (ribosomal protein L5 pseudogene 4)

RPL5P4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYM4	NM_005095.3 link	c.86-7823A>G		intron_variant	Intron 2 of 29	ENST00000314607.11	NP_005086.2	Q5VZL5-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZMYM4	ENST00000314607.11 link	c.86-7823A>G	intron_variant	Intron 2 of 29	2	NM_005095.3	ENSP00000322915.6	Q5VZL5-1
RPL5P4	ENST00000434805.1 link	n.381A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
ZMYM4	ENST00000441447.1 link	c.-11-7823A>G	intron_variant	Intron 3 of 3	5		ENSP00000397524.1	A0A0A0MSN3

Frequencies

GnomAD3 genomes

AF:

0.0689

AC:

10480

AN:

152088

Hom.:

958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0678

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.0870

Gnomad FIN

AF:

0.0697

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0182

Gnomad OTH

AF:

0.0679

GnomAD4 exome

AF:

0.0693

AC:

50650

AN:

730546

Hom.:

6900

Cov.:

AF XY:

0.0660

AC XY:

25726

AN XY:

389970

show subpopulations

African (AFR)

AF:

0.0690

AC:

1341

AN:

19430

American (AMR)

AF:

0.262

AC:

11330

AN:

43164

Ashkenazi Jewish (ASJ)

AF:

0.0354

AC:

737

AN:

20826

East Asian (EAS)

AF:

0.500

AC:

18222

AN:

36478

South Asian (SAS)

AF:

0.0804

AC:

5613

AN:

69796

European-Finnish (FIN)

AF:

0.0642

AC:

2446

AN:

38098

Middle Eastern (MID)

AF:

0.0280

AC:

AN:

2714

European-Non Finnish (NFE)

AF:

0.0186

AC:

8621

AN:

463742

Other (OTH)

AF:

0.0624

AC:

2264

AN:

36298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

2129

4258

6387

8516

10645

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

504

1008

1512

2016

2520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0691

AC:

10519

AN:

152206

Hom.:

970

Cov.:

AF XY:

0.0761

AC XY:

5660

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0682

AC:

2832

AN:

41522

American (AMR)

AF:

0.180

AC:

2756

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0334

AC:

116

AN:

3470

East Asian (EAS)

AF:

0.439

AC:

2265

AN:

5158

South Asian (SAS)

AF:

0.0875

AC:

422

AN:

4822

European-Finnish (FIN)

AF:

0.0697

AC:

740

AN:

10614

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0182

AC:

1239

AN:

68014

Other (OTH)

AF:

0.0686

AC:

145

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

430

861

1291

1722

2152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0418

Hom.:

Bravo

AF:

0.0810

Asia WGS

AF:

0.220

AC:

763

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

3.8

(source)

DANN

Benign

0.68

PhyloP100

5.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over