chr2-128721268-A-G

Variant names:

• chr2-128721268-A-G
• rs4662834
• ENST00000730281.1:n.772+23639A>G

Variant summary

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

The ENST00000730281.1(ENSG00000295469):​n.772+23639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,944 control chromosomes in the GnomAD database, including 30,460 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 0.63 (30460 hom., cov: 31)
• Consequence: ENSG00000295469 ENST00000730281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 10 publications found

Genes affected

ENSG00000295469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730281.1. 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
	ENSG00000295469	ENST00000730281.1		n.772+23639A>G		intron	N/A
	ENSG00000295469	ENST00000730282.1		n.743+23639A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95119 AN: 151828 Hom.: 30413 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.627 AC: 95219 AN: 151944 Hom.: 30460 Cov.: 31 AF XY: 0.618 AC XY: 45908 AN XY: 74242

African (AFR) AF: 0.754 AC: 31264 AN: 41474

American (AMR) AF: 0.635 AC: 9690 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2410 AN: 5152

South Asian (SAS) AF: 0.406 AC: 1950 AN: 4800

European-Finnish (FIN) AF: 0.523 AC: 5507 AN: 10532

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40123 AN: 67942

Other (OTH) AF: 0.614 AC: 1296 AN: 2112

Alfa AF: 0.597 Hom.: 120006

Bravo AF: 0.640

Asia WGS AF: 0.477 AC: 1655 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	1.2
DANN	Benign	0.37
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs4662834; hg19: chr2-129478842;