chrX-43427013-T-C

Variant names:

• chrX-43427013-T-C
• rs10521430
• ENST00000649774.1:n.619-11322T>C

Variant summary

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

The ENST00000649774.1(ENSG00000285899):​n.619-11322T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 111,952 control chromosomes in the GnomAD database, including 41 homozygotes. There are 691 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 0.021 (41 hom., 691 hem., cov: 23)
• Consequence: ENSG00000285899 ENST00000649774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 0 publications found

Genes affected

ENSG00000285899 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.066 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649774.1. 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
	ENSG00000285899	ENST00000649774.1		n.619-11322T>C		intron	N/A
	ENSG00000285899	ENST00000811237.1		n.298-11322T>C		intron	N/A
	ENSG00000285899	ENST00000811238.1		n.363-11322T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 2335 AN: 111895 Hom.: 40 Cov.: 23

Gnomad AFR AF: 0.00426

Gnomad AMI AF: 0.00291

Gnomad AMR AF: 0.0699

Gnomad ASJ AF: 0.0238

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00862

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0217

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0209 AC: 2340 AN: 111952 Hom.: 41 Cov.: 23 AF XY: 0.0203 AC XY: 691 AN XY: 34120

African (AFR) AF: 0.00425 AC: 131 AN: 30852

American (AMR) AF: 0.0702 AC: 742 AN: 10577

Ashkenazi Jewish (ASJ) AF: 0.0238 AC: 63 AN: 2643

East Asian (EAS) AF: 0.00 AC: 0 AN: 3537

South Asian (SAS) AF: 0.00901 AC: 24 AN: 2663

European-Finnish (FIN) AF: 0.0307 AC: 188 AN: 6125

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 217

European-Non Finnish (NFE) AF: 0.0217 AC: 1154 AN: 53127

Other (OTH) AF: 0.0236 AC: 36 AN: 1524

Alfa AF: 0.0241 Hom.: 203

Bravo AF: 0.0251

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.3
DANN	Benign	0.82
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10521430; hg19: chrX-43286262;