rs471205

Positions:

• chrX-67018475-C-T

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 0.44 in 110,339 control chromosomes in the GnomAD database, including 10,844 homozygotes. There are 13,865 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 0.44 (10844 hom., 13865 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 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: 0.440 AC: 48520 AN: 110289 Hom.: 10831 Cov.: 23 AF XY: 0.424 AC XY: 13815 AN XY: 32599

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.440 AC: 48585 AN: 110339 Hom.: 10844 Cov.: 23 AF XY: 0.425 AC XY: 13865 AN XY: 32659

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.433

Alfa AF: 0.285 Hom.: 17112

Bravo AF: 0.465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs471205; hg19: chrX-66238317;