X-123181616-C-T

Variant names:

• chrX-123181616-C-T
• rs3761557

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 0.454 in 110,775 control chromosomes in the GnomAD database, including 11,147 homozygotes. There are 14,537 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 0.45 (11147 hom., 14537 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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: 0.454 AC: 50235 AN: 110719 Hom.: 11135 Cov.: 23 AF XY: 0.439 AC XY: 14485 AN XY: 32965

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.319

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.454 AC: 50302 AN: 110775 Hom.: 11147 Cov.: 23 AF XY: 0.440 AC XY: 14537 AN XY: 33031

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.440

Alfa AF: 0.290 Hom.: 29028

Bravo AF: 0.486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.071
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761557; hg19: chrX-122315469;