chrX-147836750-A-G

Variant names:

• chrX-147836750-A-G
• rs4824253

Variant summary

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

The variant allele was found at a frequency of 0.312 in 110,429 control chromosomes in the GnomAD database, including 4,557 homozygotes. There are 9,695 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 0.31 (4557 hom., 9695 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.312 AC: 34468 AN: 110374 Hom.: 4558 Cov.: 22

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00253

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.312 AC: 34508 AN: 110429 Hom.: 4557 Cov.: 22 AF XY: 0.296 AC XY: 9695 AN XY: 32715

African (AFR) AF: 0.491 AC: 14831 AN: 30234

American (AMR) AF: 0.176 AC: 1826 AN: 10375

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 574 AN: 2639

East Asian (EAS) AF: 0.00254 AC: 9 AN: 3541

South Asian (SAS) AF: 0.270 AC: 703 AN: 2600

European-Finnish (FIN) AF: 0.259 AC: 1516 AN: 5862

Middle Eastern (MID) AF: 0.361 AC: 78 AN: 216

European-Non Finnish (NFE) AF: 0.272 AC: 14379 AN: 52784

Other (OTH) AF: 0.296 AC: 445 AN: 1502

Alfa AF: 0.293 Hom.: 23617

Bravo AF: 0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs4824253; hg19: chrX-146918268;