X-71189108-G-A

Position:

• chrX-71189108-G-A

Variant summary

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

The ENST00000664514.3(ENSG00000228427):​n.332-5091C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 110,730 control chromosomes in the GnomAD database, including 9,675 homozygotes. There are 15,973 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 0.48 (9675 hom., 15973 hem., cov: 23)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-5091C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664514.3	n.332-5091C>T		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.268-5091C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.322-5095C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.484 AC: 53545 AN: 110680 Hom.: 9669 Cov.: 23 AF XY: 0.484 AC XY: 15937 AN XY: 32932

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.484 AC: 53587 AN: 110730 Hom.: 9675 Cov.: 23 AF XY: 0.484 AC XY: 15973 AN XY: 32992

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.533

Alfa AF: 0.424 Hom.: 4861

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7891662; hg19: chrX-70408958;