rs5916245

Variant names:

• chrX-5743495-T-C
• rs5916245

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 0.302 in 111,042 control chromosomes in the GnomAD database, including 3,835 homozygotes. There are 9,833 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 0.30 (3835 hom., 9833 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 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: 0.302 AC: 33542 AN: 110991 Hom.: 3839 Cov.: 23

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.302 AC: 33526 AN: 111042 Hom.: 3835 Cov.: 23 AF XY: 0.295 AC XY: 9833 AN XY: 33284

African (AFR) AF: 0.199 AC: 6098 AN: 30609

American (AMR) AF: 0.343 AC: 3607 AN: 10505

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 919 AN: 2631

East Asian (EAS) AF: 0.516 AC: 1789 AN: 3465

South Asian (SAS) AF: 0.235 AC: 625 AN: 2658

European-Finnish (FIN) AF: 0.355 AC: 2093 AN: 5893

Middle Eastern (MID) AF: 0.223 AC: 48 AN: 215

European-Non Finnish (NFE) AF: 0.335 AC: 17690 AN: 52868

Other (OTH) AF: 0.289 AC: 439 AN: 1521

Alfa AF: 0.326 Hom.: 33423

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.38
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs5916245; hg19: chrX-5661536;