chrX-66759331-T-C

Position:

• chrX-66759331-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XR_938422.2(LOC105373240):​n.162+2034T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

Genes affected

LOC105373240 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373240	XR_938422.2	n.162+2034T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 72600 AN: 110929 Hom.: 20530 Cov.: 23 AF XY: 0.666 AC XY: 22066 AN XY: 33149

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.706

Alfa AF: 0.771 Hom.: 13985

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs775362; hg19: chrX-65979173;