rs6540401

Positions:

• chrX-148237293-C-A

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 0.153 in 110,217 control chromosomes in the GnomAD database, including 1,765 homozygotes. There are 4,473 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 0.15 (1765 hom., 4473 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.153 AC: 16851 AN: 110163 Hom.: 1764 Cov.: 22 AF XY: 0.137 AC XY: 4456 AN XY: 32473

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.00292

Gnomad AMR AF: 0.0750

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.00171

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.132

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.153 AC: 16872 AN: 110217 Hom.: 1765 Cov.: 22 AF XY: 0.137 AC XY: 4473 AN XY: 32537

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.00171

Gnomad4 SAS AF: 0.0635

Gnomad4 FIN AF: 0.0358

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.128

Alfa AF: 0.121 Hom.: 687

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6540401; hg19: chrX-147318813;