rs471205

Variant names:

• chrX-67018475-C-T
• rs471205

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 0.44 in 110,339 control chromosomes in the GnomAD database, including 10,844 homozygotes. There are 13,865 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 0.44 (10844 hom., 13865 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.871 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: 0.440 AC: 48520 AN: 110289 Hom.: 10831 Cov.: 23

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.440 AC: 48585 AN: 110339 Hom.: 10844 Cov.: 23 AF XY: 0.425 AC XY: 13865 AN XY: 32659

African (AFR) AF: 0.880 AC: 26658 AN: 30291

American (AMR) AF: 0.319 AC: 3310 AN: 10362

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 639 AN: 2631

East Asian (EAS) AF: 0.449 AC: 1548 AN: 3446

South Asian (SAS) AF: 0.274 AC: 707 AN: 2585

European-Finnish (FIN) AF: 0.256 AC: 1506 AN: 5873

Middle Eastern (MID) AF: 0.417 AC: 90 AN: 216

European-Non Finnish (NFE) AF: 0.253 AC: 13357 AN: 52765

Other (OTH) AF: 0.433 AC: 647 AN: 1495

Alfa AF: 0.346 Hom.: 33321

Bravo AF: 0.465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs471205; hg19: chrX-66238317;