rs9392465

Variant names:

• chr6-3162144-C-A
• rs9392465

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 0.573 in 151,812 control chromosomes in the GnomAD database, including 26,195 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 0.57 (26195 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.573 AC: 86985 AN: 151694 Hom.: 26190 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.573 AC: 87023 AN: 151812 Hom.: 26195 Cov.: 30 AF XY: 0.571 AC XY: 42386 AN XY: 74186

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.603

Alfa AF: 0.649 Hom.: 65261

Bravo AF: 0.553

Asia WGS AF: 0.494 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9392465; hg19: chr6-3162378;