X-75663162-T-G

Variant names:

• chrX-75663162-T-G
• rs5938152
• ENST00000785233.1:n.848-5018T>G

Variant summary

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

The ENST00000785233.1(ENSG00000302260):​n.848-5018T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 111,340 control chromosomes in the GnomAD database, including 193 homozygotes. There are 1,656 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 0.053 (193 hom., 1656 hem., cov: 23)
• Consequence: ENSG00000302260 ENST00000785233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 0 publications found

Genes affected

ENSG00000302260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785233.1. 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
	ENSG00000302260	ENST00000785233.1		n.848-5018T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 5898 AN: 111287 Hom.: 193 Cov.: 23

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.0299

Gnomad EAS AF: 0.0238

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0168

Gnomad NFE AF: 0.0269

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0531 AC: 5915 AN: 111340 Hom.: 193 Cov.: 23 AF XY: 0.0493 AC XY: 1656 AN XY: 33574

African (AFR) AF: 0.115 AC: 3541 AN: 30661

American (AMR) AF: 0.0263 AC: 275 AN: 10446

Ashkenazi Jewish (ASJ) AF: 0.0299 AC: 79 AN: 2646

East Asian (EAS) AF: 0.0239 AC: 85 AN: 3556

South Asian (SAS) AF: 0.133 AC: 357 AN: 2680

European-Finnish (FIN) AF: 0.0151 AC: 90 AN: 5965

Middle Eastern (MID) AF: 0.0184 AC: 4 AN: 217

European-Non Finnish (NFE) AF: 0.0269 AC: 1426 AN: 52985

Other (OTH) AF: 0.0387 AC: 58 AN: 1500

Alfa AF: 0.0431 Hom.: 1047

Bravo AF: 0.0550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.40
PhyloP100		0.18

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: rs5938152;

hg19: chrX-74882997;