chrX-12965184-A-G

Variant names:

• chrX-12965184-A-G
• rs5979778

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 0.325 in 110,621 control chromosomes in the GnomAD database, including 4,686 homozygotes. There are 10,294 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 0.32 (4686 hom., 10294 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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: 0.325 AC: 35929 AN: 110565 Hom.: 4685 Cov.: 22

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.262

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.325 AC: 35943 AN: 110621 Hom.: 4686 Cov.: 22 AF XY: 0.313 AC XY: 10294 AN XY: 32893

African (AFR) AF: 0.185 AC: 5644 AN: 30527

American (AMR) AF: 0.256 AC: 2675 AN: 10455

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 937 AN: 2611

East Asian (EAS) AF: 0.179 AC: 631 AN: 3534

South Asian (SAS) AF: 0.302 AC: 804 AN: 2666

European-Finnish (FIN) AF: 0.431 AC: 2478 AN: 5752

Middle Eastern (MID) AF: 0.258 AC: 56 AN: 217

European-Non Finnish (NFE) AF: 0.418 AC: 22026 AN: 52684

Other (OTH) AF: 0.322 AC: 484 AN: 1505

Alfa AF: 0.381 Hom.: 32820

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.7
DANN	Benign	0.90
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5979778; hg19: chrX-12983303;