9-8012418-A-G

Position:

• chr9-8012418-A-G

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 0.336 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.358

Alfa AF: 0.357 Hom.: 8681

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

Splicing

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

Publications

LitVar

Other links and lift over

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