chrX-66759331-T-C

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373240	XR_938422.2	n.162+2034T>C		intron_variant	Intron 1 of 2

Ensembl

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

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 v4.3

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;