rs3806798

Variant names:

• chr4-141636126-T-A
• rs3806798

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 0.0891 in 152,210 control chromosomes in the GnomAD database, including 781 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 0.089 (781 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 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: 0.0891 AC: 13558 AN: 152092 Hom.: 779 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0891 AC: 13564 AN: 152210 Hom.: 781 Cov.: 32 AF XY: 0.0907 AC XY: 6752 AN XY: 74416

Gnomad4 AFR AF: 0.0220

Gnomad4 AMR AF: 0.0688

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.110

Alfa AF: 0.104 Hom.: 139

Bravo AF: 0.0825

Asia WGS AF: 0.143 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806798; hg19: chr4-142557279;