chrX-144839177-G-C

Variant names:

• chrX-144839177-G-C
• rs5966270

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;