X-148803846-T-C

Variant names:

• chrX-148803846-T-C
• rs1860929
• NM_002025.4:c.1042-6030T>C

Variant summary

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

The NM_002025.4(AFF2):​c.1042-6030T>C 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 0.77 (22900 hom., 23121 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: AFF2 NM_002025.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 2 publications found

Genes affected

AFF2 (HGNC:3776): (ALF transcription elongation factor 2) This gene encodes a putative transcriptional activator that is a member of the AF4\FMR2 gene family. This gene is associated with the folate-sensitive fragile X E locus on chromosome X. A repeat polymorphism in the fragile X E locus results in silencing of this gene causing Fragile X E syndrome. Fragile X E syndrome is a form of nonsyndromic X-linked cognitive disability. In addition, this gene contains 6-25 GCC repeats that are expanded to >200 repeats in the disease state. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jul 2016]

AFF2 Gene-Disease associations (from GenCC):

• FRAXE intellectual disability

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
• non-syndromic X-linked intellectual disability

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002025.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFF2	NM_002025.4	MANE Select	c.1042-6030T>C		intron	N/A	NP_002016.2
	AFF2	NM_001169123.2		c.1030-6030T>C		intron	N/A	NP_001162594.1
	AFF2	NM_001169122.2		c.1030-6030T>C		intron	N/A	NP_001162593.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFF2	ENST00000370460.7	TSL:5 MANE Select	c.1042-6030T>C		intron	N/A	ENSP00000359489.2
	AFF2	ENST00000342251.7	TSL:1	c.1030-6030T>C		intron	N/A	ENSP00000345459.4
	AFF2	ENST00000370457.9	TSL:1	c.1042-6030T>C		intron	N/A	ENSP00000359486.6

Frequencies

GnomAD3 genomes AF: 0.766 AC: 82537 AN: 107816 Hom.: 22905 Cov.: 21

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.815

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: 0.766 AC: 82577 AN: 107869 Hom.: 22900 Cov.: 21 AF XY: 0.764 AC XY: 23121 AN XY: 30281

African (AFR) AF: 0.740 AC: 21822 AN: 29509

American (AMR) AF: 0.871 AC: 8705 AN: 9993

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2066 AN: 2602

East Asian (EAS) AF: 0.930 AC: 3101 AN: 3333

South Asian (SAS) AF: 0.873 AC: 2052 AN: 2351

European-Finnish (FIN) AF: 0.698 AC: 3815 AN: 5465

Middle Eastern (MID) AF: 0.857 AC: 180 AN: 210

European-Non Finnish (NFE) AF: 0.748 AC: 39085 AN: 52251

Other (OTH) AF: 0.815 AC: 1207 AN: 1481

Alfa AF: 0.754 Hom.: 10596

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.54
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: rs1860929; hg19: chrX-147885370;