chr4-25593908-T-C

Variant names:

• chr4-25593908-T-C
• rs1402031
• ENST00000671933.1:n.343-14803T>C

Variant summary

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

The ENST00000671933.1(ENSG00000248545):​n.343-14803T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,120 control chromosomes in the GnomAD database, including 58,296 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 0.87 (58296 hom., cov: 31)
• Consequence: ENSG00000248545 ENST00000671933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 4 publications found

Genes affected

ENSG00000248545 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671933.1. 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
	ENSG00000248545	ENST00000671933.1		n.343-14803T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132713 AN: 152002 Hom.: 58232 Cov.: 31

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.873 AC: 132836 AN: 152120 Hom.: 58296 Cov.: 31 AF XY: 0.874 AC XY: 64987 AN XY: 74344

African (AFR) AF: 0.960 AC: 39865 AN: 41534

American (AMR) AF: 0.846 AC: 12913 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2689 AN: 3472

East Asian (EAS) AF: 0.890 AC: 4586 AN: 5150

South Asian (SAS) AF: 0.908 AC: 4373 AN: 4816

European-Finnish (FIN) AF: 0.869 AC: 9191 AN: 10582

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56317 AN: 67992

Other (OTH) AF: 0.870 AC: 1837 AN: 2112

Alfa AF: 0.853 Hom.: 19402

Bravo AF: 0.878

Asia WGS AF: 0.895 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.091
DANN	Benign	0.20
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1402031; hg19: chr4-25595530;