X-71195458-A-G

Position:

• chrX-71195458-A-G

Variant summary

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

The ENST00000664514.3(ENSG00000228427):​n.331+2451T>C 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 0.507 in 107,835 control chromosomes in the GnomAD database, including 11,019 homozygotes. There are 15,058 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 0.51 (11019 hom., 15058 hem., cov: 21)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.285+2451T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.331+2451T>C		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.267+2451T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.321+2451T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.507 AC: 54596 AN: 107785 Hom.: 11010 Cov.: 21 AF XY: 0.496 AC XY: 15019 AN XY: 30295

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.507 AC: 54645 AN: 107835 Hom.: 11019 Cov.: 21 AF XY: 0.496 AC XY: 15058 AN XY: 30355

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.555

Alfa AF: 0.221 Hom.: 914

Bravo AF: 0.535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525478; hg19: chrX-70415308;