rs734329

Variant names:

• chrX-42754100-A-C
• rs734329
• ENST00000671190.1:n.183+1610T>G

Your query was ambiguous. Multiple possible variants found:

• chrX-42754100-A-C
• chrX-42754100-A-T

Variant summary

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

The ENST00000671190.1(ENSG00000287223):​n.183+1610T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 108,489 control chromosomes in the GnomAD database, including 6,131 homozygotes. There are 9,446 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 0.32 (6131 hom., 9446 hem., cov: 21)
• Consequence: ENSG00000287223 ENST00000671190.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 1 publications found

Genes affected

ENSG00000287223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671190.1. 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
	ENSG00000287223	ENST00000671190.1		n.183+1610T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.321 AC: 34822 AN: 108443 Hom.: 6125 Cov.: 21

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0819

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.322 AC: 34886 AN: 108489 Hom.: 6131 Cov.: 21 AF XY: 0.306 AC XY: 9446 AN XY: 30901

African (AFR) AF: 0.615 AC: 18130 AN: 29474

American (AMR) AF: 0.429 AC: 4369 AN: 10176

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 360 AN: 2614

East Asian (EAS) AF: 0.733 AC: 2465 AN: 3363

South Asian (SAS) AF: 0.219 AC: 539 AN: 2460

European-Finnish (FIN) AF: 0.174 AC: 979 AN: 5634

Middle Eastern (MID) AF: 0.0900 AC: 19 AN: 211

European-Non Finnish (NFE) AF: 0.140 AC: 7357 AN: 52431

Other (OTH) AF: 0.316 AC: 464 AN: 1467

Alfa AF: 0.214 Hom.: 11076

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-1.6

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: rs734329;

hg19: chrX-42613351;