rs12340987

Variant names:

• chr9-85156012-A-G
• rs12340987

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 0.188 in 152,132 control chromosomes in the GnomAD database, including 3,126 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 0.19 (3126 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.188 AC: 28527 AN: 152014 Hom.: 3117 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.188 AC: 28557 AN: 152132 Hom.: 3126 Cov.: 33 AF XY: 0.185 AC XY: 13767 AN XY: 74354

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00424

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.184

Alfa AF: 0.171 Hom.: 302

Bravo AF: 0.189

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.2
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: rs12340987; hg19: chr9-87770927;