rs775362

Variant names:

• chrX-66759331-T-C
• rs775362
• XR_938422.2:n.162+2034T>C

Variant summary

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

The XR_938422.2(LOC105373240):​n.162+2034T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (20522 hom., 22078 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: LOC105373240 XR_938422.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 4 publications found

Genes affected

LOC105373240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

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: 0.654 AC: 72600 AN: 110929 Hom.: 20530 Cov.: 23

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.702

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: 0.654 AC: 72590 AN: 110982 Hom.: 20522 Cov.: 23 AF XY: 0.665 AC XY: 22078 AN XY: 33212

African (AFR) AF: 0.139 AC: 4275 AN: 30769

American (AMR) AF: 0.832 AC: 8561 AN: 10291

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 2443 AN: 2631

East Asian (EAS) AF: 0.998 AC: 3516 AN: 3522

South Asian (SAS) AF: 0.918 AC: 2401 AN: 2616

European-Finnish (FIN) AF: 0.824 AC: 4832 AN: 5864

Middle Eastern (MID) AF: 0.747 AC: 162 AN: 217

European-Non Finnish (NFE) AF: 0.846 AC: 44744 AN: 52901

Other (OTH) AF: 0.706 AC: 1059 AN: 1501

Alfa AF: 0.763 Hom.: 32336

Bravo AF: 0.637

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.79
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs775362; hg19: chrX-65979173;