rs3027869

Variant names:

• chrX-153946086-G-A
• rs3027869

Your query was ambiguous. Multiple possible variants found:

• chrX-153946086-G-A
• chrX-153946086-G-C

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 0.212 in 110,849 control chromosomes in the GnomAD database, including 2,596 homozygotes. There are 7,315 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 0.21 (2596 hom., 7315 hem., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.212 AC: 23484 AN: 110795 Hom.: 2590 Cov.: 24

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.212 AC: 23493 AN: 110849 Hom.: 2596 Cov.: 24 AF XY: 0.221 AC XY: 7315 AN XY: 33109

African (AFR) AF: 0.115 AC: 3502 AN: 30541

American (AMR) AF: 0.424 AC: 4472 AN: 10540

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 671 AN: 2641

East Asian (EAS) AF: 0.757 AC: 2601 AN: 3435

South Asian (SAS) AF: 0.590 AC: 1534 AN: 2598

European-Finnish (FIN) AF: 0.166 AC: 980 AN: 5914

Middle Eastern (MID) AF: 0.329 AC: 71 AN: 216

European-Non Finnish (NFE) AF: 0.174 AC: 9207 AN: 52771

Other (OTH) AF: 0.270 AC: 409 AN: 1517

Alfa AF: 0.196 Hom.: 1181

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.76
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs3027869; hg19: chrX-153211538; COSMIC: COSV60078671;