X-71186069-T-C

Position:

• chrX-71186069-T-C

Variant summary

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

The ENST00000664514.3(ENSG00000228427):​n.332-2052A>G variant causes a intron, non coding transcript 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 (10689 hom., 11597 hem., cov: 17)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.286-2052A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.332-2052A>G		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.268-2052A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.322-2056A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.506 AC: 50404 AN: 99682 Hom.: 10685 Cov.: 17 AF XY: 0.490 AC XY: 11569 AN XY: 23622

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.506 AC: 50433 AN: 99708 Hom.: 10689 Cov.: 17 AF XY: 0.490 AC XY: 11597 AN XY: 23660

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.563

Alfa AF: 0.159 Hom.: 485

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6624538; hg19: chrX-70405919;