rs5906754

Variant names:

• chrX-49203767-C-T
• rs5906754

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 0.516 in 110,102 control chromosomes in the GnomAD database, including 11,948 homozygotes. There are 16,526 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 0.52 (11948 hom., 16526 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.661 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: 0.516 AC: 56774 AN: 110047 Hom.: 11956 Cov.: 22

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.516 AC: 56764 AN: 110102 Hom.: 11948 Cov.: 22 AF XY: 0.510 AC XY: 16526 AN XY: 32376

African (AFR) AF: 0.242 AC: 7347 AN: 30353

American (AMR) AF: 0.435 AC: 4497 AN: 10347

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2075 AN: 2632

East Asian (EAS) AF: 0.333 AC: 1163 AN: 3491

South Asian (SAS) AF: 0.671 AC: 1705 AN: 2542

European-Finnish (FIN) AF: 0.613 AC: 3538 AN: 5767

Middle Eastern (MID) AF: 0.702 AC: 151 AN: 215

European-Non Finnish (NFE) AF: 0.666 AC: 35050 AN: 52594

Other (OTH) AF: 0.547 AC: 819 AN: 1497

Alfa AF: 0.605 Hom.: 79207

Bravo AF: 0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.8
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs5906754; hg19: chrX-49060227;