chrX-142182644-A-G

Variant names:

• chrX-142182644-A-G
• rs5908216
• ENST00000664519.1:n.223-13063A>G

Variant summary

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

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

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

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

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

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
ENSG00000288098	ENST00000664519.1	n.223-13063A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.727 AC: 80295 AN: 110389 Hom.: 21755 Cov.: 23

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

African (AFR) AF: 0.886 AC: 26863 AN: 30308

American (AMR) AF: 0.578 AC: 6002 AN: 10376

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 1905 AN: 2639

East Asian (EAS) AF: 0.202 AC: 705 AN: 3482

South Asian (SAS) AF: 0.589 AC: 1527 AN: 2592

European-Finnish (FIN) AF: 0.605 AC: 3523 AN: 5823

Middle Eastern (MID) AF: 0.776 AC: 163 AN: 210

European-Non Finnish (NFE) AF: 0.720 AC: 38056 AN: 52835

Other (OTH) AF: 0.680 AC: 1018 AN: 1498

Alfa AF: 0.717 Hom.: 108809

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs5908216; hg19: chrX-141270430;