rs3821947

Variant names:

• chr4-4858411-A-G
• rs3821947

Your query was ambiguous. Multiple possible variants found:

• chr4-4858411-A-G
• chr4-4858411-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 0.596 in 151,932 control chromosomes in the GnomAD database, including 28,300 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 0.60 (28300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.482

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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: 0.596 AC: 90496 AN: 151814 Hom.: 28240 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.596 AC: 90613 AN: 151932 Hom.: 28300 Cov.: 32 AF XY: 0.604 AC XY: 44835 AN XY: 74258

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.567

Alfa AF: 0.501 Hom.: 19314

Bravo AF: 0.603

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3821947; hg19: chr4-4860138;