rs5905779

Variant names:

• chrX-49872019-C-G
• rs5905779

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 0.236 in 111,181 control chromosomes in the GnomAD database, including 3,067 homozygotes. There are 7,404 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 0.24 (3067 hom., 7404 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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: 0.236 AC: 26207 AN: 111127 Hom.: 3061 Cov.: 23

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0512

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.0705

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.236 AC: 26254 AN: 111181 Hom.: 3067 Cov.: 23 AF XY: 0.221 AC XY: 7404 AN XY: 33443

African (AFR) AF: 0.436 AC: 13262 AN: 30448

American (AMR) AF: 0.303 AC: 3201 AN: 10552

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 598 AN: 2636

East Asian (EAS) AF: 0.0510 AC: 180 AN: 3527

South Asian (SAS) AF: 0.0656 AC: 175 AN: 2669

European-Finnish (FIN) AF: 0.0705 AC: 421 AN: 5970

Middle Eastern (MID) AF: 0.158 AC: 34 AN: 215

European-Non Finnish (NFE) AF: 0.149 AC: 7881 AN: 52968

Other (OTH) AF: 0.222 AC: 337 AN: 1520

Alfa AF: 0.190 Hom.: 1283

Bravo AF: 0.269

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.60
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs5905779; hg19: chrX-49636622;