chr2-237478585-A-G

Variant names:

• chr2-237478585-A-G
• rs7584330
• ENST00000741027.1:n.286+4553A>G

Variant summary

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

The ENST00000741027.1(ENSG00000296651):​n.286+4553A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,086 control chromosomes in the GnomAD database, including 13,622 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 0.37 (13622 hom., cov: 32)
• Consequence: ENSG00000296651 ENST00000741027.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 52 publications found

Genes affected

ENSG00000296651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741027.1. 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
	ENSG00000296651	ENST00000741027.1		n.286+4553A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56226 AN: 151968 Hom.: 13584 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.370 AC: 56322 AN: 152086 Hom.: 13622 Cov.: 32 AF XY: 0.364 AC XY: 27086 AN XY: 74360

African (AFR) AF: 0.690 AC: 28619 AN: 41478

American (AMR) AF: 0.335 AC: 5118 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1347 AN: 5184

South Asian (SAS) AF: 0.371 AC: 1788 AN: 4820

European-Finnish (FIN) AF: 0.147 AC: 1560 AN: 10592

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16167 AN: 67950

Other (OTH) AF: 0.345 AC: 727 AN: 2108

Alfa AF: 0.277 Hom.: 31557

Bravo AF: 0.396

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.94
DANN	Benign	0.81
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7584330; hg19: chr2-238387228; COSMIC: COSV69623542;