X-5478155-A-G

Variant names:

• chrX-5478155-A-G
• rs5916072
• ENST00000721126.1:n.148+2645T>C

Variant summary

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

The ENST00000721126.1(ENSG00000294104):​n.148+2645T>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 0.57 (12833 hom., 18388 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000294104 ENST00000721126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 1 publications found

Genes affected

ENSG00000294104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721126.1. 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
	ENSG00000294104	ENST00000721126.1		n.148+2645T>C		intron	N/A
	ENSG00000294104	ENST00000721127.1		n.196+2560T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.571 AC: 62726 AN: 109920 Hom.: 12831 Cov.: 23

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.581

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: 0.571 AC: 62750 AN: 109968 Hom.: 12833 Cov.: 23 AF XY: 0.570 AC XY: 18388 AN XY: 32248

African (AFR) AF: 0.555 AC: 16836 AN: 30334

American (AMR) AF: 0.723 AC: 7397 AN: 10237

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 1598 AN: 2633

East Asian (EAS) AF: 0.502 AC: 1737 AN: 3458

South Asian (SAS) AF: 0.578 AC: 1496 AN: 2587

European-Finnish (FIN) AF: 0.538 AC: 3030 AN: 5632

Middle Eastern (MID) AF: 0.514 AC: 107 AN: 208

European-Non Finnish (NFE) AF: 0.556 AC: 29311 AN: 52709

Other (OTH) AF: 0.580 AC: 868 AN: 1497

Alfa AF: 0.576 Hom.: 5009

Bravo AF: 0.587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.053
DANN	Benign	0.40
PhyloP100		-1.4

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: rs5916072;

hg19: chrX-5396196;