rs4815682

Variant names:

• chr20-4278466-G-A
• rs4815682
• ENST00000755410.1:n.50+35704G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-4278466-G-A
• chr20-4278466-G-C
• chr20-4278466-G-T

Variant summary

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

The ENST00000755410.1(ENSG00000298420):​n.50+35704G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,896 control chromosomes in the GnomAD database, including 15,432 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 0.44 (15432 hom., cov: 31)
• Consequence: ENSG00000298420 ENST00000755410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 1 publications found

Genes affected

ENSG00000298420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755410.1. 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
	ENSG00000298420	ENST00000755410.1		n.50+35704G>A		intron	N/A
	ENSG00000298420	ENST00000755411.1		n.554+16353G>A		intron	N/A
	ENSG00000298420	ENST00000755412.1		n.73+16353G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66716 AN: 151778 Hom.: 15420 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.440 AC: 66766 AN: 151896 Hom.: 15432 Cov.: 31 AF XY: 0.444 AC XY: 32928 AN XY: 74242

African (AFR) AF: 0.377 AC: 15616 AN: 41428

American (AMR) AF: 0.482 AC: 7373 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3466

East Asian (EAS) AF: 0.873 AC: 4495 AN: 5148

South Asian (SAS) AF: 0.375 AC: 1802 AN: 4804

European-Finnish (FIN) AF: 0.476 AC: 5030 AN: 10560

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29467 AN: 67890

Other (OTH) AF: 0.454 AC: 958 AN: 2110

Alfa AF: 0.426 Hom.: 8714

Bravo AF: 0.443

Asia WGS AF: 0.601 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs4815682; hg19: chr20-4259113;