X-24247832-A-G

Variant names:

• chrX-24247832-A-G
• rs4969549
• ENST00000803232.1:n.92-46993T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000803232.1(ENSG00000304417):​n.92-46993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 109,998 control chromosomes in the GnomAD database, including 7,832 homozygotes. There are 13,248 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 0.41 (7832 hom., 13248 hem., cov: 23)
• Consequence: ENSG00000304417 ENST00000803232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 2 publications found

Genes affected

ENSG00000304417 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803232.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304417	ENST00000803232.1		n.92-46993T>C		intron	N/A
	ENSG00000304417	ENST00000803233.1		n.92-43956T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.414 AC: 45490 AN: 109944 Hom.: 7833 Cov.: 23

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.414 AC: 45495 AN: 109998 Hom.: 7832 Cov.: 23 AF XY: 0.408 AC XY: 13248 AN XY: 32434

African (AFR) AF: 0.174 AC: 5287 AN: 30420

American (AMR) AF: 0.564 AC: 5774 AN: 10229

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1145 AN: 2634

East Asian (EAS) AF: 0.479 AC: 1667 AN: 3482

South Asian (SAS) AF: 0.196 AC: 524 AN: 2669

European-Finnish (FIN) AF: 0.472 AC: 2618 AN: 5541

Middle Eastern (MID) AF: 0.412 AC: 89 AN: 216

European-Non Finnish (NFE) AF: 0.518 AC: 27279 AN: 52632

Other (OTH) AF: 0.451 AC: 679 AN: 1506

Alfa AF: 0.413 Hom.: 7958

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4969549;

hg19: chrX-24265949;