X-144839177-G-C

Position:

• chrX-144839177-G-C

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 0.371 in 110,261 control chromosomes in the GnomAD database, including 8,444 homozygotes. There are 11,395 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 0.37 (8444 hom., 11395 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.371 AC: 40843 AN: 110210 Hom.: 8438 Cov.: 22 AF XY: 0.349 AC XY: 11337 AN XY: 32456

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.371 AC: 40905 AN: 110261 Hom.: 8444 Cov.: 22 AF XY: 0.350 AC XY: 11395 AN XY: 32517

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.392

Alfa AF: 0.111 Hom.: 570

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.042
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: rs5966270; hg19: chrX-143920698;