4-25065843-C-T

Variant names:

• chr4-25065843-C-T
• rs4697534
• ENST00000774230.1:n.94-202G>A

Variant summary

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

The ENST00000774230.1(ENSG00000300816):​n.94-202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.832 in 152,220 control chromosomes in the GnomAD database, including 52,815 homozygotes. 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 0.83 (52815 hom., cov: 32)
• Consequence: ENSG00000300816 ENST00000774230.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 4 publications found

Genes affected

ENSG00000300816 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774230.1. 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
	ENSG00000300816	ENST00000774230.1		n.94-202G>A		intron	N/A
	ENSG00000300816	ENST00000774231.1		n.308-202G>A		intron	N/A
	ENSG00000300816	ENST00000774233.1		n.59-202G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126617 AN: 152102 Hom.: 52763 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.832 AC: 126723 AN: 152220 Hom.: 52815 Cov.: 32 AF XY: 0.830 AC XY: 61739 AN XY: 74416

African (AFR) AF: 0.862 AC: 35820 AN: 41542

American (AMR) AF: 0.840 AC: 12848 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2881 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3739 AN: 5168

South Asian (SAS) AF: 0.847 AC: 4088 AN: 4826

European-Finnish (FIN) AF: 0.785 AC: 8308 AN: 10584

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56235 AN: 68018

Other (OTH) AF: 0.846 AC: 1787 AN: 2112

Alfa AF: 0.835 Hom.: 100067

Bravo AF: 0.837

Asia WGS AF: 0.814 AC: 2830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4697534; hg19: chr4-25067465;