X-67185407-C-T

Variant names:

• chrX-67185407-C-T
• rs34191540

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 0.522 in 109,643 control chromosomes in the GnomAD database, including 13,464 homozygotes. There are 16,657 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 0.52 (13464 hom., 16657 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 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: 0.522 AC: 57239 AN: 109589 Hom.: 13472 Cov.: 23

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.522 AC: 57230 AN: 109643 Hom.: 13464 Cov.: 23 AF XY: 0.519 AC XY: 16657 AN XY: 32087

African (AFR) AF: 0.114 AC: 3475 AN: 30405

American (AMR) AF: 0.562 AC: 5724 AN: 10180

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 1814 AN: 2609

East Asian (EAS) AF: 0.386 AC: 1331 AN: 3448

South Asian (SAS) AF: 0.490 AC: 1266 AN: 2583

European-Finnish (FIN) AF: 0.717 AC: 4018 AN: 5602

Middle Eastern (MID) AF: 0.553 AC: 115 AN: 208

European-Non Finnish (NFE) AF: 0.728 AC: 38186 AN: 52452

Other (OTH) AF: 0.520 AC: 770 AN: 1482

Alfa AF: 0.647 Hom.: 32463

Bravo AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.79
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs34191540; hg19: chrX-66405249;