rs3904872

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;