rs5961738

Positions:

• chrX-5578052-G-A
• chrX-5578052-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0151 in 110,622 control chromosomes in the GnomAD database, including 15 homozygotes. There are 495 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 0.015 (15 hom., 495 hem., cov: 23)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0151 (1671/110622) while in subpopulation NFE AF= 0.0215 (1140/52937). AF 95% confidence interval is 0.0205. There are 15 homozygotes in gnomad4. There are 495 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5578052G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0151 AC: 1670 AN: 110575 Hom.: 15 Cov.: 23 AF XY: 0.0151 AC XY: 495 AN XY: 32851

Gnomad AFR AF: 0.00238

Gnomad AMI AF: 0.00294

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00679

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0298

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0195

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

GnomAD4 genome AF: 0.0151 AC: 1671 AN: 110622 Hom.: 15 Cov.: 23 AF XY: 0.0150 AC XY: 495 AN XY: 32908

Gnomad4 AFR AF: 0.00241

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0168

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00644

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0192

Alfa AF: 0.00125 Hom.: 666

Bravo AF: 0.0150

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5961738; hg19: chrX-5496093;