rs5956180

Variant names:

• chrX-120004093-G-T
• rs5956180
• ENST00000454625.2:n.771+6626C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454625.2(RHOXF1P1):​n.771+6626C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 111,332 control chromosomes in the GnomAD database, including 5,479 homozygotes. There are 9,240 hemizygotes in GnomAD. 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 0.28 (5479 hom., 9240 hem., cov: 23)
• Consequence: RHOXF1P1 ENST00000454625.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

RHOXF1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

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
RHOXF1P1	ENST00000454625.2	n.771+6626C>A		intron_variant	Intron 4 of 4	3
RHOXF1P1	ENST00000649154.1	n.919+6626C>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.282 AC: 31332 AN: 111278 Hom.: 5476 Cov.: 23 AF XY: 0.275 AC XY: 9205 AN XY: 33512

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.0453

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.0748

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.262

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.282 AC: 31372 AN: 111332 Hom.: 5479 Cov.: 23 AF XY: 0.275 AC XY: 9240 AN XY: 33576

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.0748

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.268

Alfa AF: 0.201 Hom.: 1601

Bravo AF: 0.311

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.037
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5956180; hg19: chrX-119138050;