rs3821949

Positions:

• chr4-4858675-G-A
• chr4-4858675-G-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 0.321 in 151,588 control chromosomes in the GnomAD database, including 8,812 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 0.32 (8812 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48603 AN: 151474 Hom.: 8780 Cov.: 30

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.321 AC: 48689 AN: 151588 Hom.: 8812 Cov.: 30 AF XY: 0.320 AC XY: 23732 AN XY: 74050

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.302

Alfa AF: 0.249 Hom.: 6573

Bravo AF: 0.329

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3821949; hg19: chr4-4860402;