rs321045

Variant names:

• chrX-78412867-C-A
• rs321045

Your query was ambiguous. Multiple possible variants found:

• chrX-78412867-C-A
• chrX-78412867-C-G

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 0.37 in 107,746 control chromosomes in the GnomAD database, including 6,851 homozygotes. There are 10,914 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 0.37 (6851 hom., 10914 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.371 AC: 39909 AN: 107697 Hom.: 6858 Cov.: 21

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.445

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.370 AC: 39884 AN: 107746 Hom.: 6851 Cov.: 21 AF XY: 0.361 AC XY: 10914 AN XY: 30232

African (AFR) AF: 0.0957 AC: 2899 AN: 30295

American (AMR) AF: 0.407 AC: 4015 AN: 9861

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1250 AN: 2578

East Asian (EAS) AF: 0.248 AC: 853 AN: 3441

South Asian (SAS) AF: 0.147 AC: 373 AN: 2530

European-Finnish (FIN) AF: 0.564 AC: 3023 AN: 5360

Middle Eastern (MID) AF: 0.445 AC: 93 AN: 209

European-Non Finnish (NFE) AF: 0.517 AC: 26533 AN: 51370

Other (OTH) AF: 0.378 AC: 546 AN: 1446

Alfa AF: 0.258 Hom.: 1270

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Other links and lift over

dbSNP: rs321045; hg19: chrX-77668364;