ENST00000419129.1:n.299-3906G>A

Variant names:

• chr2-179281548-G-A
• rs6733818
• ENST00000419129.1:n.299-3906G>A

Variant summary

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

The ENST00000419129.1(ENSG00000237477):​n.299-3906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,596 control chromosomes in the GnomAD database, including 22,292 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 0.53 (22292 hom., cov: 32)
• Consequence: ENSG00000237477 ENST00000419129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 4 publications found

Genes affected

ENSG00000237477 (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 = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419129.1. 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
	ENSG00000237477	ENST00000419129.1	TSL:4	n.299-3906G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80592 AN: 151476 Hom.: 22271 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.532 AC: 80656 AN: 151596 Hom.: 22292 Cov.: 32 AF XY: 0.533 AC XY: 39483 AN XY: 74102

African (AFR) AF: 0.418 AC: 17269 AN: 41320

American (AMR) AF: 0.436 AC: 6648 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2491 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1756 AN: 5152

South Asian (SAS) AF: 0.500 AC: 2397 AN: 4798

European-Finnish (FIN) AF: 0.657 AC: 6862 AN: 10446

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41190 AN: 67862

Other (OTH) AF: 0.556 AC: 1169 AN: 2104

Alfa AF: 0.578 Hom.: 6157

Bravo AF: 0.507

Asia WGS AF: 0.400 AC: 1391 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.089
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6733818;

hg19: chr2-180146275;