rs5916397

Variant names:

• chrX-6485911-A-T
• rs5916397

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.128 in 110,056 control chromosomes in the GnomAD database, including 700 homozygotes. There are 3,698 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 0.13 (700 hom., 3698 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 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: 0.128 AC: 14110 AN: 110007 Hom.: 700 Cov.: 23 AF XY: 0.114 AC XY: 3689 AN XY: 32417

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.128 AC: 14123 AN: 110056 Hom.: 700 Cov.: 23 AF XY: 0.114 AC XY: 3698 AN XY: 32476

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.0810

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.132

Alfa AF: 0.138 Hom.: 755

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5916397; hg19: chrX-6403952;