rs2341539

Variant names:

• chrX-71249332-G-A
• rs2341539
• ENST00000373981.5:c.*111C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-71249332-G-A
• chrX-71249332-G-C
• chrX-71249332-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000373981.5(ZMYM3):​c.*111C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 1.0 (38646 hom., 32788 hem., cov: 23)
  • Exomes 𝑓: 0.99 (343739 hom. 324548 hem.)
  • Failed GnomAD Quality Control
• Consequence: ZMYM3 ENST00000373981.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 3 publications found

Genes affected

ZMYM3 (HGNC:13054): (zinc finger MYM-type containing 3) This gene is located on the X chromosome and is subject to X inactivation. It is highly conserved in vertebrates and most abundantly expressed in the brain. The encoded protein is a component of histone deacetylase-containing multiprotein complexes that function through modifying chromatin structure to keep genes silent. A chromosomal translocation (X;13) involving this gene is associated with X-linked cognitive disability. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2010]

ZMYM3 Gene-Disease associations (from GenCC):

• intellectual developmental disorder, X-linked 112

  Inheritance: XL Classification: MODERATE Submitted by: G2P
• intellectual disability

  Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics
• syndromic intellectual disability

  Inheritance: XL Classification: NO_KNOWN Submitted by: Illumina

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZMYM3	NM_201599.3	c.1470+129C>T		intron_variant	Intron 7 of 24	ENST00000314425.9	NP_963893.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZMYM3	ENST00000314425.9	c.1470+129C>T		intron_variant	Intron 7 of 24	1	NM_201599.3	ENSP00000322845.5

Frequencies

GnomAD3 genomes AF: 0.997 AC: 110298 AN: 110666 Hom.: 38650 Cov.: 23

Gnomad AFR AF: 0.999

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.998

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.999

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.995 AC: 1015674 AN: 1020971 Hom.: 343739 Cov.: 42 AF XY: 0.995 AC XY: 324548 AN XY: 326173

African (AFR) AF: 0.999 AC: 23445 AN: 23460

American (AMR) AF: 0.999 AC: 22373 AN: 22390

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 15535 AN: 15546

East Asian (EAS) AF: 1.00 AC: 27761 AN: 27761

South Asian (SAS) AF: 0.999 AC: 43531 AN: 43572

European-Finnish (FIN) AF: 1.00 AC: 36620 AN: 36627

Middle Eastern (MID) AF: 0.999 AC: 3853 AN: 3855

European-Non Finnish (NFE) AF: 0.994 AC: 799837 AN: 804904

Other (OTH) AF: 0.997 AC: 42719 AN: 42856

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.997 AC: 110354 AN: 110720 Hom.: 38646 Cov.: 23 AF XY: 0.997 AC XY: 32788 AN XY: 32876

African (AFR) AF: 0.999 AC: 30372 AN: 30391

American (AMR) AF: 0.998 AC: 10378 AN: 10402

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2638 AN: 2639

East Asian (EAS) AF: 1.00 AC: 3525 AN: 3525

South Asian (SAS) AF: 1.00 AC: 2582 AN: 2582

European-Finnish (FIN) AF: 1.00 AC: 5847 AN: 5847

Middle Eastern (MID) AF: 0.995 AC: 215 AN: 216

European-Non Finnish (NFE) AF: 0.994 AC: 52607 AN: 52926

Other (OTH) AF: 0.999 AC: 1509 AN: 1511

Alfa AF: 0.996 Hom.: 9205

Bravo AF: 0.997

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.68
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2341539; hg19: chrX-70469182;