rs6636767

Positions:

• chrX-142608847-G-A

Variant summary

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

The ENST00000664519.1(ENSG00000288098):​n.533-14214G>A 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 0.14 in 110,623 control chromosomes in the GnomAD database, including 900 homozygotes. There are 4,348 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 0.14 (900 hom., 4348 hem., cov: 23)
• Consequence: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373345	XR_938605.2	n.91-14214G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664519.1	n.533-14214G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 15507 AN: 110567 Hom.: 901 Cov.: 23 AF XY: 0.132 AC XY: 4344 AN XY: 32837

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.221

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.140 AC: 15507 AN: 110623 Hom.: 900 Cov.: 23 AF XY: 0.132 AC XY: 4348 AN XY: 32903

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0695

Gnomad4 SAS AF: 0.0715

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.159

Alfa AF: 0.144 Hom.: 909

Bravo AF: 0.139

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6636767; hg19: chrX-141696633;