9-8012418-A-G

Variant names:

• chr9-8012418-A-G
• rs12682851

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 0.336 in 152,002 control chromosomes in the GnomAD database, including 9,395 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 0.34 (9395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.336 AC: 51033 AN: 151882 Hom.: 9390 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.336 AC: 51049 AN: 152002 Hom.: 9395 Cov.: 32 AF XY: 0.338 AC XY: 25128 AN XY: 74282

African (AFR) AF: 0.193 AC: 7995 AN: 41482

American (AMR) AF: 0.428 AC: 6532 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3470

East Asian (EAS) AF: 0.551 AC: 2849 AN: 5170

South Asian (SAS) AF: 0.463 AC: 2231 AN: 4814

European-Finnish (FIN) AF: 0.334 AC: 3527 AN: 10562

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25005 AN: 67944

Other (OTH) AF: 0.358 AC: 753 AN: 2104

Alfa AF: 0.353 Hom.: 18593

Bravo AF: 0.340

Asia WGS AF: 0.475 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.56
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs12682851; hg19: chr9-8012418; COSMIC: COSV52394304;