ENST00000431862.1:n.228-23385A>G

Variant names:

• chr1-159387894-T-C
• rs4446959
• ENST00000431862.1:n.228-23385A>G

Variant summary

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

The ENST00000431862.1(ENSG00000228560):​n.228-23385A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,048 control chromosomes in the GnomAD database, including 20,250 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 0.46 (20250 hom., cov: 32)
• Consequence: ENSG00000228560 ENST00000431862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 17 publications found

Genes affected

ENSG00000228560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431862.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228560	ENST00000431862.1	TSL:1	n.228-23385A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70441 AN: 151930 Hom.: 20201 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.464 AC: 70547 AN: 152048 Hom.: 20250 Cov.: 32 AF XY: 0.463 AC XY: 34400 AN XY: 74348

African (AFR) AF: 0.821 AC: 34013 AN: 41452

American (AMR) AF: 0.443 AC: 6758 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3464

East Asian (EAS) AF: 0.335 AC: 1732 AN: 5172

South Asian (SAS) AF: 0.295 AC: 1421 AN: 4822

European-Finnish (FIN) AF: 0.347 AC: 3673 AN: 10576

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20771 AN: 67978

Other (OTH) AF: 0.400 AC: 844 AN: 2110

Alfa AF: 0.360 Hom.: 23691

Bravo AF: 0.487

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4446959; hg19: chr1-159357684;