chrX-147547380-A-C

Variant names:

• chrX-147547380-A-C
• rs5905078

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 0.286 in 110,973 control chromosomes in the GnomAD database, including 3,487 homozygotes. There are 9,304 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 0.29 (3487 hom., 9304 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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: 0.286 AC: 31669 AN: 110922 Hom.: 3483 Cov.: 23

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.257

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.286 AC: 31683 AN: 110973 Hom.: 3487 Cov.: 23 AF XY: 0.280 AC XY: 9304 AN XY: 33237

African (AFR) AF: 0.342 AC: 10444 AN: 30577

American (AMR) AF: 0.382 AC: 3978 AN: 10425

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 386 AN: 2644

East Asian (EAS) AF: 0.526 AC: 1826 AN: 3469

South Asian (SAS) AF: 0.413 AC: 1091 AN: 2642

European-Finnish (FIN) AF: 0.207 AC: 1223 AN: 5916

Middle Eastern (MID) AF: 0.262 AC: 55 AN: 210

European-Non Finnish (NFE) AF: 0.229 AC: 12112 AN: 52908

Other (OTH) AF: 0.269 AC: 404 AN: 1502

Alfa AF: 0.248 Hom.: 1495

Bravo AF: 0.306

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs5905078; hg19: chrX-146628898;