rs4830487

Variant names:

• chrX-13112365-T-C
• rs4830487
• ENST00000840939.1:n.348+26562T>C

Variant summary

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

The ENST00000840939.1(ENSG00000289596):​n.348+26562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 110,606 control chromosomes in the GnomAD database, including 5,333 homozygotes. There are 11,460 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 0.34 (5333 hom., 11460 hem., cov: 22)
• Consequence: ENSG00000289596 ENST00000840939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 publications found

Genes affected

ENSG00000289596 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840939.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289596	ENST00000840939.1		n.348+26562T>C		intron	N/A
	ENSG00000289596	ENST00000840940.1		n.220+26562T>C		intron	N/A
	ENSG00000289596	ENST00000840941.1		n.149+26567T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.340 AC: 37585 AN: 110552 Hom.: 5328 Cov.: 22

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.340 AC: 37597 AN: 110606 Hom.: 5333 Cov.: 22 AF XY: 0.349 AC XY: 11460 AN XY: 32838

African (AFR) AF: 0.118 AC: 3630 AN: 30637

American (AMR) AF: 0.509 AC: 5278 AN: 10371

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 940 AN: 2642

East Asian (EAS) AF: 0.606 AC: 2125 AN: 3505

South Asian (SAS) AF: 0.587 AC: 1524 AN: 2596

European-Finnish (FIN) AF: 0.482 AC: 2758 AN: 5722

Middle Eastern (MID) AF: 0.315 AC: 68 AN: 216

European-Non Finnish (NFE) AF: 0.391 AC: 20613 AN: 52730

Other (OTH) AF: 0.319 AC: 480 AN: 1507

Alfa AF: 0.376 Hom.: 46861

Bravo AF: 0.341

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.017
DANN	Benign	0.62
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs4830487; hg19: chrX-13130484;