rs3806929

Variant names:

• chr5-171418055-G-A
• rs3806929

Your query was ambiguous. Multiple possible variants found:

• chr5-171418055-G-A
• chr5-171418055-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 0.403 in 151,686 control chromosomes in the GnomAD database, including 12,366 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 0.40 (12366 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.403 AC: 61136 AN: 151564 Hom.: 12344 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.403 AC: 61201 AN: 151686 Hom.: 12366 Cov.: 31 AF XY: 0.404 AC XY: 29919 AN XY: 74092

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.415

Alfa AF: 0.392 Hom.: 5556

Bravo AF: 0.405

Asia WGS AF: 0.458 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806929; hg19: chr5-170845059; COSMIC: COSV51125646;