X-101690351-G-C

Variant names:

• chrX-101690351-G-C
• rs6621148
• ENST00000788550.1:n.239+5358G>C

Variant summary

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

The ENST00000788550.1(ENSG00000302652):​n.239+5358G>C 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 0.78 (24039 hom., 25442 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000302652 ENST00000788550.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 0 publications found

Genes affected

ENSG00000302652 (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: ENST00000788550.1. 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
	ENSG00000302652	ENST00000788550.1		n.239+5358G>C		intron	N/A
	ENSG00000302652	ENST00000788551.1		n.449+5358G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 86257 AN: 110525 Hom.: 24041 Cov.: 23

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.770

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: 0.780 AC: 86306 AN: 110580 Hom.: 24039 Cov.: 23 AF XY: 0.776 AC XY: 25442 AN XY: 32792

African (AFR) AF: 0.868 AC: 26409 AN: 30434

American (AMR) AF: 0.844 AC: 8802 AN: 10425

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 1929 AN: 2628

East Asian (EAS) AF: 0.838 AC: 2928 AN: 3496

South Asian (SAS) AF: 0.840 AC: 2180 AN: 2596

European-Finnish (FIN) AF: 0.613 AC: 3584 AN: 5846

Middle Eastern (MID) AF: 0.748 AC: 160 AN: 214

European-Non Finnish (NFE) AF: 0.730 AC: 38531 AN: 52774

Other (OTH) AF: 0.771 AC: 1145 AN: 1486

Alfa AF: 0.611 Hom.: 2537

Bravo AF: 0.801

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
PhyloP100		-0.12

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: rs6621148;

hg19: chrX-100945351;