X-12899668-C-T

Variant names:

• chrX-12899668-C-T
• rs178998

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 0.477 in 110,079 control chromosomes in the GnomAD database, including 9,306 homozygotes. There are 15,532 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 (9306 hom., 15532 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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: 0.477 AC: 52453 AN: 110024 Hom.: 9307 Cov.: 22

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.479

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.477 AC: 52493 AN: 110079 Hom.: 9306 Cov.: 22 AF XY: 0.480 AC XY: 15532 AN XY: 32349

African (AFR) AF: 0.584 AC: 17623 AN: 30192

American (AMR) AF: 0.551 AC: 5703 AN: 10357

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1301 AN: 2632

East Asian (EAS) AF: 0.829 AC: 2868 AN: 3458

South Asian (SAS) AF: 0.612 AC: 1591 AN: 2599

European-Finnish (FIN) AF: 0.391 AC: 2250 AN: 5755

Middle Eastern (MID) AF: 0.481 AC: 104 AN: 216

European-Non Finnish (NFE) AF: 0.381 AC: 20084 AN: 52709

Other (OTH) AF: 0.476 AC: 712 AN: 1495

Alfa AF: 0.424 Hom.: 12048

Bravo AF: 0.500

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.74
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs178998; hg19: chrX-12917787;