rs5908216

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664519.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000288098	ENST00000664519.1		n.223-13063A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5908216;

hg19: chrX-141270430;