X-144839177-G-C

Variant names:

• chrX-144839177-G-C
• rs5966270

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.371 AC: 40843 AN: 110210 Hom.: 8438 Cov.: 22

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

African (AFR) AF: 0.766 AC: 23035 AN: 30065

American (AMR) AF: 0.414 AC: 4289 AN: 10348

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 651 AN: 2639

East Asian (EAS) AF: 0.521 AC: 1789 AN: 3434

South Asian (SAS) AF: 0.334 AC: 870 AN: 2604

European-Finnish (FIN) AF: 0.108 AC: 634 AN: 5893

Middle Eastern (MID) AF: 0.310 AC: 65 AN: 210

European-Non Finnish (NFE) AF: 0.167 AC: 8850 AN: 52894

Other (OTH) AF: 0.392 AC: 586 AN: 1495

Alfa AF: 0.111 Hom.: 570

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.042
DANN	Benign	0.38
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs5966270; hg19: chrX-143920698;