rs6636767

Variant names:

• chrX-142608847-G-A
• rs6636767
• ENST00000664519.1:n.533-14214G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664519.1(ENSG00000288098):​n.533-14214G>A variant causes a intron 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: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 0 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105373345	XR_938605.2	n.91-14214G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288098	ENST00000664519.1	n.533-14214G>A		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.140 AC: 15507 AN: 110567 Hom.: 901 Cov.: 23

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

African (AFR) AF: 0.121 AC: 3686 AN: 30486

American (AMR) AF: 0.123 AC: 1272 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 569 AN: 2633

East Asian (EAS) AF: 0.0695 AC: 242 AN: 3482

South Asian (SAS) AF: 0.0715 AC: 187 AN: 2617

European-Finnish (FIN) AF: 0.126 AC: 730 AN: 5802

Middle Eastern (MID) AF: 0.210 AC: 44 AN: 210

European-Non Finnish (NFE) AF: 0.159 AC: 8419 AN: 52839

Other (OTH) AF: 0.159 AC: 239 AN: 1507

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6636767; hg19: chrX-141696633;