rs4474149

Variant names:

• chrX-123496525-T-C
• rs4474149

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;