rs4892427

Variant names:

• chrX-76138369-T-C
• rs4892427
• ENST00000844515.1:n.354+3937A>G

Variant summary

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

The ENST00000844515.1(ENSG00000309870):​n.354+3937A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 110,771 control chromosomes in the GnomAD database, including 9,554 homozygotes. There are 14,689 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 0.46 (9554 hom., 14689 hem., cov: 22)
• Consequence: ENSG00000309870 ENST00000844515.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 1 publications found

Genes affected

ENSG00000309870 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844515.1. 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
	ENSG00000309870	ENST00000844515.1		n.354+3937A>G		intron	N/A
	ENSG00000309870	ENST00000844516.1		n.278+3937A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.455 AC: 50418 AN: 110718 Hom.: 9563 Cov.: 22

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.455 AC: 50415 AN: 110771 Hom.: 9554 Cov.: 22 AF XY: 0.445 AC XY: 14689 AN XY: 33001

African (AFR) AF: 0.208 AC: 6350 AN: 30546

American (AMR) AF: 0.451 AC: 4682 AN: 10387

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 1830 AN: 2628

East Asian (EAS) AF: 0.110 AC: 390 AN: 3532

South Asian (SAS) AF: 0.360 AC: 936 AN: 2603

European-Finnish (FIN) AF: 0.523 AC: 3070 AN: 5875

Middle Eastern (MID) AF: 0.600 AC: 129 AN: 215

European-Non Finnish (NFE) AF: 0.602 AC: 31810 AN: 52819

Other (OTH) AF: 0.505 AC: 755 AN: 1494

Alfa AF: 0.557 Hom.: 17887

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.29
PhyloP100		0.22

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: rs4892427;

hg19: chrX-75358204;