rs5975493

Variant names:

• chrX-135042148-C-G
• rs5975493

Your query was ambiguous. Multiple possible variants found:

• chrX-135042148-C-G
• chrX-135042148-C-T

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 0.415 in 109,066 control chromosomes in the GnomAD database, including 7,163 homozygotes. There are 12,393 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 0.42 (7163 hom., 12393 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.416 AC: 45302 AN: 109018 Hom.: 7166 Cov.: 21

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.415 AC: 45313 AN: 109066 Hom.: 7163 Cov.: 21 AF XY: 0.395 AC XY: 12393 AN XY: 31414

African (AFR) AF: 0.397 AC: 11866 AN: 29861

American (AMR) AF: 0.394 AC: 4017 AN: 10204

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1143 AN: 2609

East Asian (EAS) AF: 0.227 AC: 784 AN: 3456

South Asian (SAS) AF: 0.139 AC: 351 AN: 2519

European-Finnish (FIN) AF: 0.387 AC: 2178 AN: 5634

Middle Eastern (MID) AF: 0.379 AC: 80 AN: 211

European-Non Finnish (NFE) AF: 0.458 AC: 23993 AN: 52409

Other (OTH) AF: 0.417 AC: 622 AN: 1491

Alfa AF: 0.244 Hom.: 1092

Bravo AF: 0.420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.87
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs5975493; hg19: chrX-134176178;