X-9957954-G-T

Variant names:

• chrX-9957954-G-T
• rs5934725
• ENST00000850985.1:c.4585-9383G>T

Variant summary

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

The ENST00000850985.1(ENSG00000310579):​c.4585-9383G>T 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 0.51 (11043 hom., 15604 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000310579 ENST00000850985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 0 publications found

Genes affected

ENSG00000310579 (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: ENST00000850985.1. 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
	ENSG00000310579	ENST00000850985.1		c.4585-9383G>T		intron	N/A	ENSP00000521067.1

Frequencies

GnomAD3 genomes AF: 0.513 AC: 55812 AN: 108792 Hom.: 11030 Cov.: 21

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.514

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: 0.513 AC: 55881 AN: 108843 Hom.: 11043 Cov.: 21 AF XY: 0.499 AC XY: 15604 AN XY: 31269

African (AFR) AF: 0.700 AC: 20817 AN: 29756

American (AMR) AF: 0.514 AC: 5190 AN: 10103

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 894 AN: 2627

East Asian (EAS) AF: 0.419 AC: 1445 AN: 3451

South Asian (SAS) AF: 0.423 AC: 1078 AN: 2548

European-Finnish (FIN) AF: 0.459 AC: 2530 AN: 5515

Middle Eastern (MID) AF: 0.414 AC: 89 AN: 215

European-Non Finnish (NFE) AF: 0.436 AC: 22860 AN: 52480

Other (OTH) AF: 0.521 AC: 768 AN: 1475

Alfa AF: 0.467 Hom.: 44431

Bravo AF: 0.529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.33

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: rs5934725;

hg19: chrX-9925994;