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

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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
ZMYM4	ENST00000441447.1 link	c.-11-7823A>G	intron_variant	Intron 3 of 3	5		ENSP00000397524.1	A0A0A0MSN3
RPL5P4	ENST00000434805.1 link	n.381A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6

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

Gnomad4 AFR exome

AF:

0.0690

Gnomad4 AMR exome

AF:

0.262

Gnomad4 ASJ exome

AF:

0.0354

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.0804

Gnomad4 FIN exome

AF:

0.0642

Gnomad4 NFE exome

AF:

0.0186

Gnomad4 OTH exome

AF:

0.0624

GnomAD4 genome

AF:

0.0691

AC:

10519

AN:

152206

Hom.:

970

Cov.:

AF XY:

0.0761

AC XY:

5660

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0682

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.0334

Gnomad4 EAS

AF:

0.439

Gnomad4 SAS

AF:

0.0875

Gnomad4 FIN

AF:

0.0697

Gnomad4 NFE

AF:

0.0182

Gnomad4 OTH

AF:

0.0686

Alfa

AF:

0.0408

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

DANN

Benign

0.68

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over