chrX-53717173-C-T

Variant names:

• chrX-53717173-C-T
• rs6638366

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 0.412 in 109,437 control chromosomes in the GnomAD database, including 8,081 homozygotes. There are 13,060 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 0.41 (8081 hom., 13060 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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: 0.412 AC: 45086 AN: 109379 Hom.: 8084 Cov.: 22 AF XY: 0.411 AC XY: 13043 AN XY: 31713

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.412 AC: 45095 AN: 109437 Hom.: 8081 Cov.: 22 AF XY: 0.411 AC XY: 13060 AN XY: 31781

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.443

Alfa AF: 0.480 Hom.: 7009

Bravo AF: 0.397

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.81
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6638366; hg19: chrX-53744116;