rs1209026

chrX-150474583-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_005491.5(MAMLD1):c.2040+781C>T variant causes a intron 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 0.80 (25048 hom., 26586 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAMLD1 NM_005491.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541

Genes affected

MAMLD1 (HGNC:2568): (mastermind like domain containing 1) This gene encodes a mastermind-like domain containing protein. This protein may function as a transcriptional co-activator. Mutations in this gene are the cause of X-linked hypospadias type 2. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 25056 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAMLD1	NM_005491.5	c.2040+781C>T		intron_variant		ENST00000370401.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAMLD1	ENST00000370401.7	c.2040+781C>T		intron_variant		5	NM_005491.5	A2

Frequencies

GnomAD3 genomes AF: 0.800 AC: 88460 AN: 110618 Hom.: 25056 Cov.: 23 AF XY: 0.808 AC XY: 26558 AN XY: 32850

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.804

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.799 AC: 88470 AN: 110671 Hom.: 25048 Cov.: 23 AF XY: 0.808 AC XY: 26586 AN XY: 32913

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.839

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.956

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.807

Alfa AF: 0.826 Hom.: 7048

Bravo AF: 0.791

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1209026; hg19: chrX-149642855;