rs760109

Positions:

• chrX-151384050-A-G

Variant summary

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

The ENST00000668689.1(ENSG00000287918):​n.1266+11827T>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 0.339 in 111,276 control chromosomes in the GnomAD database, including 5,853 homozygotes. There are 11,158 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 0.34 (5853 hom., 11158 hem., cov: 23)
• Consequence: ENST00000668689.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

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 (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668689.1	n.1266+11827T>C		intron_variant, non_coding_transcript_variant
	ENST00000664896.1	n.319+11827T>C		intron_variant, non_coding_transcript_variant
	ENST00000664935.1	n.588+12381T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.339 AC: 37711 AN: 111222 Hom.: 5847 Cov.: 23 AF XY: 0.334 AC XY: 11151 AN XY: 33434

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.339 AC: 37720 AN: 111276 Hom.: 5853 Cov.: 23 AF XY: 0.333 AC XY: 11158 AN XY: 33498

Gnomad4 AFR AF: 0.0852

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.337

Alfa AF: 0.448 Hom.: 28035

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760109; hg19: chrX-150552522;