1-35325676-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005095.3(ZMYM4):c.85+271C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 151,874 control chromosomes in the GnomAD database, including 1,014 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 0.072 (1014 hom., cov: 32)
• Consequence: ZMYM4 NM_005095.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZMYM4	NM_005095.3	c.85+271C>G		intron_variant		ENST00000314607.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZMYM4	ENST00000314607.11	c.85+271C>G		intron_variant		2	NM_005095.3	P1
ZMYM4	ENST00000441447.1	c.-12+271C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10904 AN: 151756 Hom.: 1009 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.00665

Gnomad MID AF: 0.0194

Gnomad NFE AF: 0.00939

Gnomad OTH AF: 0.0537

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

GnomAD4 genome AF: 0.0720 AC: 10934 AN: 151874 Hom.: 1014 Cov.: 32 AF XY: 0.0711 AC XY: 5279 AN XY: 74202

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.0782

Gnomad4 SAS AF: 0.0901

Gnomad4 FIN AF: 0.00665

Gnomad4 NFE AF: 0.00938

Gnomad4 OTH AF: 0.0541

Alfa AF: 0.0119 Hom.: 14

Bravo AF: 0.0786

Asia WGS AF: 0.0950 AC: 328 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.012
Dann	Benign	0.62

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: rs10493071; hg19: chr1-35791277;