9-108856646-A-G

Variant names:

• chr9-108856646-A-G
• rs11787880

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 0.471 in 166,928 control chromosomes in the GnomAD database, including 19,318 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 0.46 (16922 hom., cov: 32)
  • Exomes 𝑓: 0.56 (2396 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.462 AC: 70153 AN: 151808 Hom.: 16910 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.454

GnomAD4 exome AF: 0.561 AC: 8414 AN: 15002 Hom.: 2396 Cov.: 0 AF XY: 0.562 AC XY: 4020 AN XY: 7148

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.750 AC: 6 AN: 8

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.561 AC: 8259 AN: 14710

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 80 AN: 160

Other (OTH) AF: 0.563 AC: 63 AN: 112

GnomAD4 genome AF: 0.462 AC: 70188 AN: 151926 Hom.: 16922 Cov.: 32 AF XY: 0.465 AC XY: 34498 AN XY: 74240

African (AFR) AF: 0.341 AC: 14140 AN: 41440

American (AMR) AF: 0.430 AC: 6560 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3466

East Asian (EAS) AF: 0.498 AC: 2555 AN: 5134

South Asian (SAS) AF: 0.443 AC: 2133 AN: 4810

European-Finnish (FIN) AF: 0.571 AC: 6029 AN: 10550

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.519 AC: 35288 AN: 67938

Other (OTH) AF: 0.455 AC: 962 AN: 2112

Alfa AF: 0.491 Hom.: 15986

Bravo AF: 0.449

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.34
PhyloP100		0.11
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11787880; hg19: chr9-111618926;