rs45631657

Positions:

• chrX-147858144-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 70 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.147858144T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0331 AC: 3672 AN: 110794 Hom.: 70 Cov.: 22 AF XY: 0.0320 AC XY: 1056 AN XY: 32982

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

Gnomad4 AFR AF: 0.00659

Gnomad4 AMR AF: 0.0239

Gnomad4 ASJ AF: 0.0322

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0101

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0480

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45631657; hg19: chrX-146939662;