ENST00000655369.1:n.222+3025G>T

Variant names:

• chr1-233862124-C-A
• rs923975
• ENST00000655369.1:n.222+3025G>T

Variant summary

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

The ENST00000655369.1(ENSG00000286666):​n.222+3025G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,046 control chromosomes in the GnomAD database, including 18,809 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 0.48 (18809 hom., cov: 32)
• Consequence: ENSG00000286666 ENST00000655369.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 2 publications found

Genes affected

ENSG00000286666 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655369.1. 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
	ENSG00000286666	ENST00000655369.1		n.222+3025G>T		intron	N/A
	ENSG00000306050	ENST00000814968.1		n.248+6306G>T		intron	N/A
	ENSG00000286666	ENST00000815093.1		n.247-2313G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73706 AN: 151928 Hom.: 18805 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.485 AC: 73717 AN: 152046 Hom.: 18809 Cov.: 32 AF XY: 0.485 AC XY: 36038 AN XY: 74290

African (AFR) AF: 0.336 AC: 13924 AN: 41482

American (AMR) AF: 0.378 AC: 5771 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3468

East Asian (EAS) AF: 0.522 AC: 2694 AN: 5160

South Asian (SAS) AF: 0.477 AC: 2294 AN: 4808

European-Finnish (FIN) AF: 0.624 AC: 6590 AN: 10566

Middle Eastern (MID) AF: 0.521 AC: 151 AN: 290

European-Non Finnish (NFE) AF: 0.572 AC: 38897 AN: 67990

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.522 Hom.: 52259

Bravo AF: 0.457

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs923975; hg19: chr1-233997870;