rs3761796

Variant names:

• chr6-106327046-A-G
• rs3761796

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0136 AC: 566 AN: 41570

American (AMR) AF: 0.194 AC: 2964 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.144 AC: 748 AN: 5190

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4822

European-Finnish (FIN) AF: 0.0174 AC: 185 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1996 AN: 68030

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0373 Hom.: 353

Bravo AF: 0.0640

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.87
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs3761796; hg19: chr6-106774921;