chrX-148237293-C-A

Variant names:

• chrX-148237293-C-A
• rs6540401

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;