rs3761796

Variant names:

• chr6-106327046-A-G
• rs3761796

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;