rs6525476

Positions:

• chrX-71191415-C-G

Variant summary

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

The ENST00000664514.3(ENSG00000228427):​n.331+6494G>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 0.509 in 110,429 control chromosomes in the GnomAD database, including 10,928 homozygotes. There are 16,602 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 (10928 hom., 16602 hem., cov: 22)
• Consequence: ENST00000664514.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985688	XR_001755878.2	n.285+6494G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664514.3	n.331+6494G>C		intron_variant, non_coding_transcript_variant
	ENST00000450860.1	n.267+6494G>C		intron_variant, non_coding_transcript_variant		3
	ENST00000652147.2	n.321+6494G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.509 AC: 56175 AN: 110375 Hom.: 10920 Cov.: 22 AF XY: 0.507 AC XY: 16556 AN XY: 32639

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.509 AC: 56229 AN: 110429 Hom.: 10928 Cov.: 22 AF XY: 0.508 AC XY: 16602 AN XY: 32703

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.562

Alfa AF: 0.457 Hom.: 3246

Bravo AF: 0.535

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6525476; hg19: chrX-70411265;