X-123181616-C-T

Variant names:

• chrX-123181616-C-T
• rs3761557

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 0.454 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

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

African (AFR) AF: 0.884 AC: 26789 AN: 30300

American (AMR) AF: 0.415 AC: 4375 AN: 10535

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 745 AN: 2630

East Asian (EAS) AF: 0.425 AC: 1487 AN: 3496

South Asian (SAS) AF: 0.314 AC: 822 AN: 2614

European-Finnish (FIN) AF: 0.288 AC: 1705 AN: 5914

Middle Eastern (MID) AF: 0.321 AC: 68 AN: 212

European-Non Finnish (NFE) AF: 0.254 AC: 13436 AN: 52906

Other (OTH) AF: 0.440 AC: 657 AN: 1494

Alfa AF: 0.323 Hom.: 41619

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3761557; hg19: chrX-122315469;