4-148669429-G-A

Variant names:

• chr4-148669429-G-A
• rs2358469
• ENST00000661928.1:n.222+124845G>A

Variant summary

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

The ENST00000661928.1(ENSG00000287292):​n.222+124845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,038 control chromosomes in the GnomAD database, including 15,748 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 0.42 (15748 hom., cov: 32)
• Consequence: ENSG00000287292 ENST00000661928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 5 publications found

Genes affected

ENSG00000287292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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: ENST00000661928.1. 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
	ENSG00000287292	ENST00000661928.1		n.222+124845G>A		intron	N/A
	ENSG00000305747	ENST00000812762.1		n.155+10903C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64134 AN: 151918 Hom.: 15745 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.422 AC: 64161 AN: 152038 Hom.: 15748 Cov.: 32 AF XY: 0.418 AC XY: 31048 AN XY: 74308

African (AFR) AF: 0.188 AC: 7807 AN: 41496

American (AMR) AF: 0.347 AC: 5299 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3466

East Asian (EAS) AF: 0.349 AC: 1798 AN: 5158

South Asian (SAS) AF: 0.492 AC: 2373 AN: 4824

European-Finnish (FIN) AF: 0.483 AC: 5091 AN: 10546

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38847 AN: 67966

Other (OTH) AF: 0.417 AC: 879 AN: 2106

Alfa AF: 0.530 Hom.: 45304

Bravo AF: 0.399

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.80
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2358469; hg19: chr4-149590581;