rs17410

Variant names:

• chrX-144939673-T-C
• rs17410

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.478 in 111,420 control chromosomes in the GnomAD database, including 9,360 homozygotes. There are 15,732 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 0.48 (9360 hom., 15732 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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: 0.478 AC: 53190 AN: 111367 Hom.: 9356 Cov.: 24 AF XY: 0.467 AC XY: 15689 AN XY: 33613

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.478 AC: 53246 AN: 111420 Hom.: 9360 Cov.: 24 AF XY: 0.467 AC XY: 15732 AN XY: 33676

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.493

Alfa AF: 0.464 Hom.: 3648

Bravo AF: 0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17410; hg19: chrX-144021193;