rs45631657

Variant names:

• chrX-147858144-T-C
• rs45631657

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0331 in 110,849 control chromosomes in the GnomAD database, including 70 homozygotes. There are 1,056 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 0.033 (70 hom., 1056 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0331 (3672/110849) while in subpopulation NFE AF = 0.0501 (2653/52944). AF 95% confidence interval is 0.0485. There are 70 homozygotes in GnomAd4. There are 1056 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 70 gene

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: 0.0331 AC: 3672 AN: 110794 Hom.: 70 Cov.: 22

Gnomad AFR AF: 0.00661

Gnomad AMI AF: 0.0162

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0322

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0101

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0630

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0486

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

GnomAD4 genome AF: 0.0331 AC: 3672 AN: 110849 Hom.: 70 Cov.: 22 AF XY: 0.0320 AC XY: 1056 AN XY: 33047

African (AFR) AF: 0.00659 AC: 201 AN: 30487

American (AMR) AF: 0.0239 AC: 248 AN: 10381

Ashkenazi Jewish (ASJ) AF: 0.0322 AC: 85 AN: 2636

East Asian (EAS) AF: 0.00 AC: 0 AN: 3496

South Asian (SAS) AF: 0.0101 AC: 26 AN: 2579

European-Finnish (FIN) AF: 0.0609 AC: 361 AN: 5929

Middle Eastern (MID) AF: 0.0691 AC: 15 AN: 217

European-Non Finnish (NFE) AF: 0.0501 AC: 2653 AN: 52944

Other (OTH) AF: 0.0480 AC: 72 AN: 1501

Alfa AF: 0.0410 Hom.: 219

Bravo AF: 0.0302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.51
DANN	Benign	0.40
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs45631657; hg19: chrX-146939662;