rs3904872

Variant names:

• chr20-4331506-A-G
• rs3904872
• ENST00000755410.1:n.51-8409A>G

Your query was ambiguous. Multiple possible variants found:

• chr20-4331506-A-G
• chr20-4331506-A-T

Variant summary

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

The ENST00000755410.1(ENSG00000298420):​n.51-8409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,130 control chromosomes in the GnomAD database, including 27,538 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 0.59 (27538 hom., cov: 32)
• Consequence: ENSG00000298420 ENST00000755410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298420	ENST00000755410.1	n.51-8409A>G		intron_variant	Intron 1 of 3
ENSG00000298420	ENST00000755411.1	n.555-8409A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89585 AN: 152012 Hom.: 27523 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.589 AC: 89639 AN: 152130 Hom.: 27538 Cov.: 32 AF XY: 0.597 AC XY: 44386 AN XY: 74368

African (AFR) AF: 0.428 AC: 17774 AN: 41494

American (AMR) AF: 0.579 AC: 8857 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2245 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2397 AN: 5174

South Asian (SAS) AF: 0.649 AC: 3122 AN: 4812

European-Finnish (FIN) AF: 0.775 AC: 8202 AN: 10588

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45153 AN: 67996

Other (OTH) AF: 0.566 AC: 1194 AN: 2110

Alfa AF: 0.586 Hom.: 3281

Bravo AF: 0.564

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.63
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs3904872; hg19: chr20-4312153;