rs6644385

Variant names:

• chrX-861671-C-T
• rs6644385

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 0.487 in 148,634 control chromosomes in the GnomAD database, including 20,369 homozygotes. There are 35,704 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 0.49 (20369 hom., 35704 hem., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 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: 0.486 AC: 72229 AN: 148516 Hom.: 20340 Cov.: 29

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.487 AC: 72312 AN: 148634 Hom.: 20369 Cov.: 29 AF XY: 0.493 AC XY: 35704 AN XY: 72432

African (AFR) AF: 0.400 AC: 16340 AN: 40898

American (AMR) AF: 0.508 AC: 7500 AN: 14766

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1551 AN: 3426

East Asian (EAS) AF: 0.945 AC: 4832 AN: 5114

South Asian (SAS) AF: 0.716 AC: 3324 AN: 4644

European-Finnish (FIN) AF: 0.481 AC: 4912 AN: 10208

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.488 AC: 32376 AN: 66390

Other (OTH) AF: 0.509 AC: 1039 AN: 2042

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.60
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs6644385; hg19: chrX-822406;