chrX-137182822-C-A

Variant names:

• chrX-137182822-C-A
• rs4829605

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.86 (30212 hom., 24310 hem., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.865 AC: 91061 AN: 105287 Hom.: 30216 Cov.: 19

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.961

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.891

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.865 AC: 91096 AN: 105334 Hom.: 30212 Cov.: 19 AF XY: 0.867 AC XY: 24310 AN XY: 28044

African (AFR) AF: 0.566 AC: 16466 AN: 29099

American (AMR) AF: 0.937 AC: 9057 AN: 9670

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 2525 AN: 2560

East Asian (EAS) AF: 0.999 AC: 3294 AN: 3297

South Asian (SAS) AF: 0.986 AC: 2196 AN: 2228

European-Finnish (FIN) AF: 0.998 AC: 4892 AN: 4904

Middle Eastern (MID) AF: 0.961 AC: 199 AN: 207

European-Non Finnish (NFE) AF: 0.985 AC: 50542 AN: 51291

Other (OTH) AF: 0.892 AC: 1261 AN: 1413

Alfa AF: 0.923 Hom.: 33635

Bravo AF: 0.852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4829605; hg19: chrX-136264981;