rs638376

Variant names:

• chrX-114998678-T-C
• rs638376

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 0.529 in 110,204 control chromosomes in the GnomAD database, including 13,322 homozygotes. There are 16,615 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 0.53 (13322 hom., 16615 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 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: 0.529 AC: 58293 AN: 110154 Hom.: 13321 Cov.: 22

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.529 AC: 58338 AN: 110204 Hom.: 13322 Cov.: 22 AF XY: 0.512 AC XY: 16615 AN XY: 32468

African (AFR) AF: 0.889 AC: 26869 AN: 30224

American (AMR) AF: 0.427 AC: 4408 AN: 10335

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1191 AN: 2628

East Asian (EAS) AF: 0.150 AC: 518 AN: 3456

South Asian (SAS) AF: 0.489 AC: 1257 AN: 2568

European-Finnish (FIN) AF: 0.349 AC: 2051 AN: 5870

Middle Eastern (MID) AF: 0.467 AC: 100 AN: 214

European-Non Finnish (NFE) AF: 0.399 AC: 21019 AN: 52716

Other (OTH) AF: 0.483 AC: 732 AN: 1515

Alfa AF: 0.447 Hom.: 32628

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs638376; hg19: chrX-114233241;