rs4830105

Variant names:

• chrX-128921593-G-T
• rs4830105
• ENST00000653849.1:n.1436-86917C>A

Variant summary

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

The ENST00000653849.1(ENSG00000225689):​n.1436-86917C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 111,248 control chromosomes in the GnomAD database, including 5,737 homozygotes. There are 11,848 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 0.36 (5737 hom., 11848 hem., cov: 24)
• Consequence: ENSG00000225689 ENST00000653849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 0 publications found

Genes affected

ENSG00000225689 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653849.1. 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
	ENSG00000225689	ENST00000653849.1		n.1436-86917C>A		intron	N/A
	ENSG00000225689	ENST00000660383.1		n.567+110757C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 39978 AN: 111194 Hom.: 5730 Cov.: 24

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.360 AC: 40030 AN: 111248 Hom.: 5737 Cov.: 24 AF XY: 0.354 AC XY: 11848 AN XY: 33494

African (AFR) AF: 0.545 AC: 16691 AN: 30624

American (AMR) AF: 0.259 AC: 2721 AN: 10526

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 730 AN: 2644

East Asian (EAS) AF: 0.164 AC: 579 AN: 3535

South Asian (SAS) AF: 0.206 AC: 551 AN: 2679

European-Finnish (FIN) AF: 0.356 AC: 2091 AN: 5880

Middle Eastern (MID) AF: 0.239 AC: 51 AN: 213

European-Non Finnish (NFE) AF: 0.300 AC: 15907 AN: 52948

Other (OTH) AF: 0.329 AC: 501 AN: 1523

Alfa AF: 0.333 Hom.: 2198

Bravo AF: 0.360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		0.32

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: rs4830105;

hg19: chrX-128055571;