1-35325676-C-G

Variant names:

• chr1-35325676-C-G
• rs10493071
• NM_005095.3:c.85+271C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005095.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYM4	NM_005095.3	MANE Select	c.85+271C>G		intron	N/A	NP_005086.2
	ZMYM4	NM_001375653.1		c.94+271C>G		intron	N/A	NP_001362582.1
	ZMYM4	NM_001350138.2		c.-12+271C>G		intron	N/A	NP_001337067.1	Q5VZL5-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYM4	ENST00000314607.11	TSL:2 MANE Select	c.85+271C>G		intron	N/A	ENSP00000322915.6	Q5VZL5-1
	ZMYM4	ENST00000933225.1		c.85+271C>G		intron	N/A	ENSP00000603284.1
	ZMYM4	ENST00000933226.1		c.85+271C>G		intron	N/A	ENSP00000603285.1

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

African (AFR) AF: 0.211 AC: 8728 AN: 41432

American (AMR) AF: 0.0340 AC: 518 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.0782 AC: 405 AN: 5182

South Asian (SAS) AF: 0.0901 AC: 432 AN: 4794

European-Finnish (FIN) AF: 0.00665 AC: 70 AN: 10528

Middle Eastern (MID) AF: 0.0243 AC: 7 AN: 288

European-Non Finnish (NFE) AF: 0.00938 AC: 637 AN: 67912

Other (OTH) AF: 0.0541 AC: 114 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.012
DANN	Benign	0.62
PhyloP100		-2.6
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: rs10493071; hg19: chr1-35791277;