rs5908216

Positions:

• chrX-142182644-A-G

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.223-13063A>G 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 0.73 (21749 hom., 23165 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664519.1	n.223-13063A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.727 AC: 80295 AN: 110389 Hom.: 21755 Cov.: 23 AF XY: 0.709 AC XY: 23118 AN XY: 32619

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.686

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: 0.727 AC: 80329 AN: 110441 Hom.: 21749 Cov.: 23 AF XY: 0.709 AC XY: 23165 AN XY: 32681

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.680

Alfa AF: 0.707 Hom.: 80006

Bravo AF: 0.725

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5908216; hg19: chrX-141270430;