rs5935438

Variant names:

• chrX-12894903-G-C
• rs5935438
• ENST00000827469.1:n.115-1509C>G

Variant summary

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

The ENST00000827469.1(ENSG00000307619):​n.115-1509C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 110,417 control chromosomes in the GnomAD database, including 6,686 homozygotes. There are 12,697 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 0.40 (6686 hom., 12697 hem., cov: 22)
• Consequence: ENSG00000307619 ENST00000827469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 7 publications found

Genes affected

ENSG00000307619 (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 (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827469.1. 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
	ENSG00000307619	ENST00000827469.1		n.115-1509C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.403 AC: 44515 AN: 110364 Hom.: 6682 Cov.: 22

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.403 AC: 44542 AN: 110417 Hom.: 6686 Cov.: 22 AF XY: 0.388 AC XY: 12697 AN XY: 32691

African (AFR) AF: 0.437 AC: 13232 AN: 30300

American (AMR) AF: 0.340 AC: 3530 AN: 10393

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 635 AN: 2621

East Asian (EAS) AF: 0.171 AC: 605 AN: 3540

South Asian (SAS) AF: 0.334 AC: 881 AN: 2636

European-Finnish (FIN) AF: 0.432 AC: 2489 AN: 5757

Middle Eastern (MID) AF: 0.358 AC: 78 AN: 218

European-Non Finnish (NFE) AF: 0.424 AC: 22368 AN: 52773

Other (OTH) AF: 0.368 AC: 553 AN: 1503

Alfa AF: 0.421 Hom.: 2863

Bravo AF: 0.398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.42
PhyloP100		0.047

Splicing

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

Other links and lift over

dbSNP: rs5935438; hg19: chrX-12913022;