rs3807032

chr6-30076002-C-Gchr6-30076002-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 0.131 in 603,504 control chromosomes in the GnomAD database, including 8,293 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 0.19 (4240 hom., cov: 33)
  • Exomes 𝑓: 0.11 (4053 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.188 AC: 28549 AN: 152058 Hom.: 4232 Cov.: 33

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.112 AC: 50682 AN: 451326 Hom.: 4053 AF XY: 0.112 AC XY: 26816 AN XY: 238410

Gnomad4 AFR exome AF: 0.403

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.166

Gnomad4 EAS exome AF: 0.171

Gnomad4 SAS exome AF: 0.152

Gnomad4 FIN exome AF: 0.0320

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.188 AC: 28587 AN: 152178 Hom.: 4240 Cov.: 33 AF XY: 0.183 AC XY: 13603 AN XY: 74432

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0264

Gnomad4 NFE AF: 0.0854

Gnomad4 OTH AF: 0.210

Alfa AF: 0.0391 Hom.: 38

Bravo AF: 0.216

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	0.11
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: rs3807032; hg19: chr6-30043779;