rs4474149

chrX-123496525-T-C

Variant summary

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

The variant allele was found at a frequency of 0.356 in 110,762 control chromosomes in the GnomAD database, including 5,174 homozygotes. There are 11,439 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 0.36 (5174 hom., 11439 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 39378 AN: 110709 Hom.: 5170 Cov.: 22 AF XY: 0.346 AC XY: 11413 AN XY: 32965

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.356 AC: 39403 AN: 110762 Hom.: 5174 Cov.: 22 AF XY: 0.346 AC XY: 11439 AN XY: 33028

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.363

Alfa AF: 0.352 Hom.: 3927

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.5
Dann	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4474149; hg19: chrX-122630376;