rs9386463

Variant names:

• chr6-105646182-A-G
• rs9386463

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 0.411 in 152,030 control chromosomes in the GnomAD database, including 15,026 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 0.41 (15026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62555 AN: 151912 Hom.: 15025 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.411 AC: 62557 AN: 152030 Hom.: 15026 Cov.: 32 AF XY: 0.414 AC XY: 30738 AN XY: 74290

African (AFR) AF: 0.160 AC: 6626 AN: 41498

American (AMR) AF: 0.586 AC: 8932 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1068 AN: 5176

South Asian (SAS) AF: 0.440 AC: 2122 AN: 4826

European-Finnish (FIN) AF: 0.463 AC: 4879 AN: 10548

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35346 AN: 67950

Other (OTH) AF: 0.461 AC: 972 AN: 2108

Alfa AF: 0.492 Hom.: 69417

Bravo AF: 0.410

Asia WGS AF: 0.363 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.4
DANN	Benign	0.65
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs9386463; hg19: chr6-106094057;