rs12010481

chrX-148019383-T-CchrX-148019383-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152578.3(FMR1NB):c.633-5482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 111,965 control chromosomes in the GnomAD database, including 2,344 homozygotes. There are 5,735 hemizygotes in GnomAD. 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 0.18 (2344 hom., 5735 hem., cov: 23)
• Consequence: FMR1NB NM_152578.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

Genes affected

FMR1NB (HGNC:26372): (FMR1 neighbor) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FMR1NB	NM_152578.3	c.633-5482T>C		intron_variant		ENST00000370467.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FMR1NB	ENST00000370467.8	c.633-5482T>C		intron_variant		1	NM_152578.3	P1
FMR1NB	ENST00000489034.2	c.122-5482T>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 20562 AN: 111912 Hom.: 2344 Cov.: 23 AF XY: 0.167 AC XY: 5710 AN XY: 34104

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.0612

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00140

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.184 AC: 20581 AN: 111965 Hom.: 2344 Cov.: 23 AF XY: 0.168 AC XY: 5735 AN XY: 34167

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00140

Gnomad4 SAS AF: 0.0704

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.176

Alfa AF: 0.142 Hom.: 847

Bravo AF: 0.201

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.8
Dann	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs12010481; hg19: chrX-147100903;