chr9-6365683-A-C

Position:

• chr9-6365683-A-C

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 0.343 in 152,038 control chromosomes in the GnomAD database, including 9,278 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 (9278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

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 = 0.374 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: 0.343 AC: 52108 AN: 151920 Hom.: 9274 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.343 AC: 52124 AN: 152038 Hom.: 9278 Cov.: 32 AF XY: 0.348 AC XY: 25847 AN XY: 74302

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.365

Alfa AF: 0.333 Hom.: 3239

Bravo AF: 0.335

Asia WGS AF: 0.268 AC: 931 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	0.88
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719725; hg19: chr9-6365683;