3-129200625-G-A

Variant names:

• chr3-129200625-G-A
• rs2101155
• ENST00000691714.3:n.428+16153G>A

Variant summary

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

The ENST00000691714.3(ENSG00000289469):​n.428+16153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,996 control chromosomes in the GnomAD database, including 53,546 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 0.81 (53546 hom., cov: 30)
• Consequence: ENSG00000289469 ENST00000691714.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 1 publications found

Genes affected

ENSG00000289469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691714.3. 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
	ENSG00000289469	ENST00000691714.3		n.428+16153G>A		intron	N/A
	ENSG00000289469	ENST00000759375.1		n.77+16782G>A		intron	N/A
	ENSG00000289469	ENST00000759376.1		n.395-14523G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122597 AN: 151878 Hom.: 53552 Cov.: 30

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.807 AC: 122618 AN: 151996 Hom.: 53546 Cov.: 30 AF XY: 0.810 AC XY: 60173 AN XY: 74310

African (AFR) AF: 0.438 AC: 18111 AN: 41366

American (AMR) AF: 0.872 AC: 13314 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3329 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4567 AN: 5154

South Asian (SAS) AF: 0.845 AC: 4072 AN: 4818

European-Finnish (FIN) AF: 0.955 AC: 10114 AN: 10596

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.973 AC: 66159 AN: 68002

Other (OTH) AF: 0.845 AC: 1787 AN: 2116

Alfa AF: 0.879 Hom.: 7275

Bravo AF: 0.784

Asia WGS AF: 0.831 AC: 2893 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	3.2
DANN	Benign	0.60
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2101155; hg19: chr3-128919468;