rs6529220

Variant names:

• chrX-127556073-C-T
• rs6529220
• ENST00000755052.1:n.708+31466G>A

Variant summary

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

The ENST00000755052.1(ENSG00000260683):​n.708+31466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 109,370 control chromosomes in the GnomAD database, including 12,710 homozygotes. There are 15,495 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 0.50 (12710 hom., 15495 hem., cov: 21)
• Consequence: ENSG00000260683 ENST00000755052.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 0 publications found

Genes affected

ENSG00000260683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755052.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260683	ENST00000755052.1		n.708+31466G>A		intron	N/A
	ENSG00000260683	ENST00000755053.1		n.354+31466G>A		intron	N/A
	ENSG00000260683	ENST00000755054.1		n.172+31466G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.503 AC: 55001 AN: 109327 Hom.: 12698 Cov.: 21

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.504 AC: 55068 AN: 109370 Hom.: 12710 Cov.: 21 AF XY: 0.488 AC XY: 15495 AN XY: 31754

African (AFR) AF: 0.897 AC: 26935 AN: 30023

American (AMR) AF: 0.515 AC: 5245 AN: 10188

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 769 AN: 2614

East Asian (EAS) AF: 0.0539 AC: 187 AN: 3471

South Asian (SAS) AF: 0.252 AC: 645 AN: 2555

European-Finnish (FIN) AF: 0.419 AC: 2347 AN: 5595

Middle Eastern (MID) AF: 0.343 AC: 74 AN: 216

European-Non Finnish (NFE) AF: 0.340 AC: 17846 AN: 52540

Other (OTH) AF: 0.468 AC: 701 AN: 1497

Alfa AF: 0.461 Hom.: 3871

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.31
PhyloP100		-0.96

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6529220;

hg19: chrX-126690054;