X-148500637-TGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC-TGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC

Variant names:

• chrX-148500637-TGCCGCCGCCGCC-T
• rs193922937
• NM_002025.4:c.-425_-414delCGCCGCCGCCGC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_002025.4(AFF2):​c.-425_-414delCGCCGCCGCCGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 73,738 control chromosomes in the GnomAD database, including 6 homozygotes. There are 107 hemizygotes in GnomAD. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0060 (6 hom., 104 hem., cov: 0)
  • Exomes 𝑓: 0.0049 (0 hom. 3 hem.)
• Consequence: AFF2 NM_002025.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.80
• Publications: 1 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

ENSG00000237741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.006 (439/73124) while in subpopulation EAS AF = 0.0362 (72/1991). AF 95% confidence interval is 0.0294. There are 6 homozygotes in GnomAd4. There are 104 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 XL gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFF2	NM_002025.4	MANE Select	c.-425_-414delCGCCGCCGCCGC		5_prime_UTR	Exon 1 of 21	NP_002016.2
	AFF2	NM_001169123.2		c.-425_-414delCGCCGCCGCCGC		5_prime_UTR	Exon 1 of 21	NP_001162594.1
	AFF2	NM_001169122.2		c.-425_-414delCGCCGCCGCCGC		5_prime_UTR	Exon 1 of 20	NP_001162593.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFF2	ENST00000370460.7	TSL:5 MANE Select	c.-425_-414delCGCCGCCGCCGC		5_prime_UTR	Exon 1 of 21	ENSP00000359489.2
	AFF2	ENST00000342251.7	TSL:1	c.-460_-449delGCCGCCGCCGCC		upstream_gene	N/A	ENSP00000345459.4
	ENSG00000237741	ENST00000456981.1	TSL:3	n.-34_-23delGGCGGCGGCGGC		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.00602 AC: 440 AN: 73139 Hom.: 6 Cov.: 0

Gnomad AFR AF: 0.00188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00675

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.00863

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00980

Gnomad NFE AF: 0.00442

Gnomad OTH AF: 0.00847

GnomAD4 exome AF: 0.00489 AC: 3 AN: 614 Hom.: 0 AF XY: 0.0183 AC XY: 3 AN XY: 164

African (AFR) AF: 0.00 AC: 0 AN: 1

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00556 AC: 3 AN: 540

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 60

Other (OTH) AF: 0.00 AC: 0 AN: 10

GnomAD4 genome AF: 0.00600 AC: 439 AN: 73124 Hom.: 6 Cov.: 0 AF XY: 0.00672 AC XY: 104 AN XY: 15466

African (AFR) AF: 0.00188 AC: 37 AN: 19705

American (AMR) AF: 0.00675 AC: 45 AN: 6670

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 96 AN: 1996

East Asian (EAS) AF: 0.0362 AC: 72 AN: 1991

South Asian (SAS) AF: 0.00874 AC: 12 AN: 1373

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1921

Middle Eastern (MID) AF: 0.0109 AC: 1 AN: 92

European-Non Finnish (NFE) AF: 0.00442 AC: 168 AN: 38018

Other (OTH) AF: 0.00840 AC: 8 AN: 952

Alfa AF: 0.00 Hom.: 154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs193922937; hg19: chrX-147582157;