rs6526959

Variant names:

• chrX-30204678-C-A
• rs6526959
• ENST00000796024.1:n.591+8655G>T

Variant summary

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

The ENST00000796024.1(ENSG00000303603):​n.591+8655G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 111,033 control chromosomes in the GnomAD database, including 11,085 homozygotes. There are 16,373 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 (11085 hom., 16373 hem., cov: 24)
• Consequence: ENSG00000303603 ENST00000796024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 0 publications found

Genes affected

ENSG00000303603 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303603	ENST00000796024.1	n.591+8655G>T		intron_variant	Intron 3 of 6
ENSG00000303603	ENST00000796025.1	n.572+8655G>T		intron_variant	Intron 3 of 5
ENSG00000303603	ENST00000796026.1	n.563+8655G>T		intron_variant	Intron 3 of 3
ENSG00000303603	ENST00000796028.1	n.563+8655G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.515 AC: 57142 AN: 110977 Hom.: 11086 Cov.: 24

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.515 AC: 57180 AN: 111033 Hom.: 11085 Cov.: 24 AF XY: 0.492 AC XY: 16373 AN XY: 33297

African (AFR) AF: 0.573 AC: 17517 AN: 30561

American (AMR) AF: 0.453 AC: 4744 AN: 10463

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1259 AN: 2634

East Asian (EAS) AF: 0.0375 AC: 135 AN: 3597

South Asian (SAS) AF: 0.245 AC: 655 AN: 2672

European-Finnish (FIN) AF: 0.469 AC: 2737 AN: 5840

Middle Eastern (MID) AF: 0.437 AC: 94 AN: 215

European-Non Finnish (NFE) AF: 0.550 AC: 29088 AN: 52873

Other (OTH) AF: 0.459 AC: 689 AN: 1502

Alfa AF: 0.525 Hom.: 19395

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.35
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs6526959; hg19: chrX-30222795;