rs5968255

Variant names:

• chrX-83999684-T-C
• rs5968255

Your query was ambiguous. Multiple possible variants found:

• chrX-83999684-T-C
• chrX-83999684-T-G

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 0.127 in 111,247 control chromosomes in the GnomAD database, including 873 homozygotes. There are 4,257 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 (873 hom., 4257 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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: 0.127 AC: 14155 AN: 111188 Hom.: 872 Cov.: 22

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.0966

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0675

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.127 AC: 14160 AN: 111247 Hom.: 873 Cov.: 22 AF XY: 0.127 AC XY: 4257 AN XY: 33485

African (AFR) AF: 0.0861 AC: 2647 AN: 30728

American (AMR) AF: 0.136 AC: 1425 AN: 10456

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 354 AN: 2635

East Asian (EAS) AF: 0.534 AC: 1845 AN: 3458

South Asian (SAS) AF: 0.266 AC: 700 AN: 2630

European-Finnish (FIN) AF: 0.141 AC: 839 AN: 5931

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.115 AC: 6092 AN: 52987

Other (OTH) AF: 0.116 AC: 176 AN: 1522

Alfa AF: 0.124 Hom.: 12151

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs5968255; hg19: chrX-83254692;