rs17145638

Variant names:

• chrX-40026377-T-C
• rs17145638

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 0.107 in 110,470 control chromosomes in the GnomAD database, including 495 homozygotes. There are 3,340 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 0.11 (495 hom., 3340 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.149 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: 0.107 AC: 11836 AN: 110420 Hom.: 494 Cov.: 22

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.0821

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0748

Gnomad EAS AF: 0.0186

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0837

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.107 AC: 11838 AN: 110470 Hom.: 495 Cov.: 22 AF XY: 0.102 AC XY: 3340 AN XY: 32716

African (AFR) AF: 0.0821 AC: 2496 AN: 30399

American (AMR) AF: 0.155 AC: 1597 AN: 10278

Ashkenazi Jewish (ASJ) AF: 0.0748 AC: 197 AN: 2632

East Asian (EAS) AF: 0.0183 AC: 65 AN: 3544

South Asian (SAS) AF: 0.0961 AC: 249 AN: 2591

European-Finnish (FIN) AF: 0.144 AC: 828 AN: 5738

Middle Eastern (MID) AF: 0.0780 AC: 17 AN: 218

European-Non Finnish (NFE) AF: 0.117 AC: 6168 AN: 52879

Other (OTH) AF: 0.109 AC: 165 AN: 1509

Alfa AF: 0.119 Hom.: 6966

Bravo AF: 0.109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs17145638; hg19: chrX-39885630;