rs3806794

chr4-74364585-C-Achr4-74364585-C-Gchr4-74364585-C-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 0.0477 in 152,190 control chromosomes in the GnomAD database, including 195 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 0.048 (195 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0881 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: 0.0478 AC: 7271 AN: 152072 Hom.: 194 Cov.: 31

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.0952

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0477 AC: 7267 AN: 152190 Hom.: 195 Cov.: 31 AF XY: 0.0483 AC XY: 3590 AN XY: 74396

Gnomad4 AFR AF: 0.0490

Gnomad4 AMR AF: 0.0301

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.0711

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0418 Hom.: 212

Bravo AF: 0.0457

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.85
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806794; hg19: chr4-75230302;