rs3761796

chr6-106327046-A-G

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 0.0463 in 152,320 control chromosomes in the GnomAD database, including 479 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 0.046 (479 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 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: 0.0462 AC: 7038 AN: 152202 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0463 AC: 7053 AN: 152320 Hom.: 479 Cov.: 33 AF XY: 0.0485 AC XY: 3610 AN XY: 74486

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0293

Gnomad4 OTH AF: 0.0625

Alfa AF: 0.0348 Hom.: 107

Bravo AF: 0.0640

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	13
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761796; hg19: chr6-106774921;