Genetic Variant NM_005095.3: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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