chrX-43753461-G-A

Variant names:

• chrX-43753461-G-A
• rs6609257

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 110,616 control chromosomes in the GnomAD database, including 9,732 homozygotes. There are 15,390 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 (9732 hom., 15390 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 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: 0.477 AC: 52721 AN: 110565 Hom.: 9740 Cov.: 22

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.477 AC: 52726 AN: 110616 Hom.: 9732 Cov.: 22 AF XY: 0.468 AC XY: 15390 AN XY: 32878

African (AFR) AF: 0.264 AC: 8048 AN: 30511

American (AMR) AF: 0.536 AC: 5586 AN: 10430

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1399 AN: 2638

East Asian (EAS) AF: 0.413 AC: 1432 AN: 3471

South Asian (SAS) AF: 0.378 AC: 984 AN: 2606

European-Finnish (FIN) AF: 0.489 AC: 2859 AN: 5845

Middle Eastern (MID) AF: 0.509 AC: 109 AN: 214

European-Non Finnish (NFE) AF: 0.591 AC: 31179 AN: 52722

Other (OTH) AF: 0.483 AC: 725 AN: 1502

Alfa AF: 0.539 Hom.: 50184

Bravo AF: 0.469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.68
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs6609257; hg19: chrX-43612708;