chrX-57038379-G-A

Variant names:

• chrX-57038379-G-A
• rs204138

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 0.545 in 110,806 control chromosomes in the GnomAD database, including 14,494 homozygotes. There are 18,252 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 0.54 (14494 hom., 18252 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.545 AC: 60376 AN: 110753 Hom.: 14502 Cov.: 23

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.545 AC: 60356 AN: 110806 Hom.: 14494 Cov.: 23 AF XY: 0.553 AC XY: 18252 AN XY: 33028

African (AFR) AF: 0.114 AC: 3512 AN: 30728

American (AMR) AF: 0.552 AC: 5749 AN: 10420

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1415 AN: 2634

East Asian (EAS) AF: 0.658 AC: 2259 AN: 3434

South Asian (SAS) AF: 0.626 AC: 1634 AN: 2611

European-Finnish (FIN) AF: 0.846 AC: 4912 AN: 5807

Middle Eastern (MID) AF: 0.373 AC: 81 AN: 217

European-Non Finnish (NFE) AF: 0.748 AC: 39453 AN: 52771

Other (OTH) AF: 0.486 AC: 732 AN: 1507

Alfa AF: 0.193 Hom.: 2402

Bravo AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.45
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs204138; hg19: chrX-57064812;