chrX-144724003-T-C

Variant names:

• chrX-144724003-T-C
• rs644429

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 0.338 in 110,328 control chromosomes in the GnomAD database, including 5,063 homozygotes. There are 10,700 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 0.34 (5063 hom., 10700 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.419 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: 0.337 AC: 37215 AN: 110279 Hom.: 5057 Cov.: 22

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.393

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.338 AC: 37243 AN: 110328 Hom.: 5063 Cov.: 22 AF XY: 0.328 AC XY: 10700 AN XY: 32580

African (AFR) AF: 0.192 AC: 5848 AN: 30455

American (AMR) AF: 0.293 AC: 3039 AN: 10381

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1359 AN: 2623

East Asian (EAS) AF: 0.142 AC: 495 AN: 3496

South Asian (SAS) AF: 0.372 AC: 972 AN: 2613

European-Finnish (FIN) AF: 0.431 AC: 2470 AN: 5731

Middle Eastern (MID) AF: 0.399 AC: 85 AN: 213

European-Non Finnish (NFE) AF: 0.423 AC: 22275 AN: 52631

Other (OTH) AF: 0.365 AC: 550 AN: 1508

Alfa AF: 0.384 Hom.: 17764

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs644429; hg19: chrX-143805524;