9-108856646-A-G

Variant names:

• chr9-108856646-A-G
• rs11787880

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 0.471 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.462 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

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.561

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.563

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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.455

Alfa AF: 0.485 Hom.: 10551

Bravo AF: 0.449

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs11787880; hg19: chr9-111618926;