rs3904872

Variant names:

• chr20-4331506-A-G
• rs3904872

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.566

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3904872; hg19: chr20-4312153;