X-79325907-T-C

Variant names:

• chrX-79325907-T-C
• rs1736653

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 0.90 (31673 hom., 27936 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• 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=-1.02).

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: 0.902 AC: 97988 AN: 108579 Hom.: 31671 Cov.: 21

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.919

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: 0.903 AC: 98044 AN: 108632 Hom.: 31673 Cov.: 21 AF XY: 0.905 AC XY: 27936 AN XY: 30874

African (AFR) AF: 0.939 AC: 27934 AN: 29754

American (AMR) AF: 0.848 AC: 8678 AN: 10239

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 2427 AN: 2626

East Asian (EAS) AF: 0.999 AC: 3429 AN: 3431

South Asian (SAS) AF: 0.971 AC: 2376 AN: 2446

European-Finnish (FIN) AF: 0.882 AC: 4805 AN: 5447

Middle Eastern (MID) AF: 0.949 AC: 204 AN: 215

European-Non Finnish (NFE) AF: 0.884 AC: 46272 AN: 52341

Other (OTH) AF: 0.920 AC: 1343 AN: 1460

Alfa AF: 0.901 Hom.: 9104

Bravo AF: 0.898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.23
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs1736653; hg19: chrX-78581404;