rs4664883

Variant names:

• chr2-151018421-A-C
• rs4664883
• ENST00000409243.1:n.298+15388T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-151018421-A-C
• chr2-151018421-A-G
• chr2-151018421-A-T

Variant summary

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

The ENST00000409243.1(ENSG00000222031):​n.298+15388T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,074 control chromosomes in the GnomAD database, including 55,262 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 0.84 (55262 hom., cov: 31)
• Consequence: ENSG00000222031 ENST00000409243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 3 publications found

Genes affected

ENSG00000222031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409243.1. 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
	ENSG00000222031	ENST00000409243.1	TSL:3	n.298+15388T>G		intron	N/A
	ENSG00000222031	ENST00000812493.1		n.181+15388T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128001 AN: 151958 Hom.: 55221 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.842 AC: 128094 AN: 152074 Hom.: 55262 Cov.: 31 AF XY: 0.846 AC XY: 62858 AN XY: 74340

African (AFR) AF: 0.638 AC: 26441 AN: 41412

American (AMR) AF: 0.904 AC: 13824 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3073 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4869 AN: 5160

South Asian (SAS) AF: 0.826 AC: 3977 AN: 4814

European-Finnish (FIN) AF: 0.961 AC: 10198 AN: 10608

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62746 AN: 68008

Other (OTH) AF: 0.861 AC: 1815 AN: 2108

Alfa AF: 0.893 Hom.: 31226

Bravo AF: 0.831

Asia WGS AF: 0.870 AC: 3027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs4664883; hg19: chr2-151874935;