chrX-57041275-G-A

Variant names:

• chrX-57041275-G-A
• rs204141

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 110,297 control chromosomes in the GnomAD database, including 14,490 homozygotes. There are 18,022 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 (14490 hom., 18022 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.545 AC: 60132 AN: 110240 Hom.: 14498 Cov.: 22

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.371

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.545 AC: 60111 AN: 110297 Hom.: 14490 Cov.: 22 AF XY: 0.553 AC XY: 18022 AN XY: 32571

African (AFR) AF: 0.114 AC: 3485 AN: 30552

American (AMR) AF: 0.551 AC: 5699 AN: 10348

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1407 AN: 2621

East Asian (EAS) AF: 0.658 AC: 2258 AN: 3431

South Asian (SAS) AF: 0.623 AC: 1585 AN: 2545

European-Finnish (FIN) AF: 0.848 AC: 4911 AN: 5790

Middle Eastern (MID) AF: 0.374 AC: 79 AN: 211

European-Non Finnish (NFE) AF: 0.748 AC: 39340 AN: 52621

Other (OTH) AF: 0.490 AC: 735 AN: 1501

Alfa AF: 0.482 Hom.: 2401

Bravo AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.7
DANN	Benign	0.94
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs204141; hg19: chrX-57067708;