rs5988407

Variant names:

• chrX-821895-C-T
• rs5988407

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 0.658 in 151,950 control chromosomes in the GnomAD database, including 33,659 homozygotes. There are 48,665 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 0.66 (33659 hom., 48665 hem., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 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: 0.658 AC: 99955 AN: 151832 Hom.: 33632 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.658 AC: 100036 AN: 151950 Hom.: 33659 Cov.: 33 AF XY: 0.656 AC XY: 48665 AN XY: 74228

African (AFR) AF: 0.704 AC: 29199 AN: 41486

American (AMR) AF: 0.643 AC: 9796 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1088 AN: 5158

South Asian (SAS) AF: 0.563 AC: 2713 AN: 4818

European-Finnish (FIN) AF: 0.723 AC: 7628 AN: 10546

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45339 AN: 67928

Other (OTH) AF: 0.629 AC: 1328 AN: 2112

Bravo AF: 0.654

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs5988407; hg19: chrX-782630;