rs9402168

Variant names:

• chr6-129745591-A-G
• rs9402168

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 0.424 in 151,996 control chromosomes in the GnomAD database, including 14,422 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 0.42 (14422 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.423 AC: 64295 AN: 151878 Hom.: 14391 Cov.: 30

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.424 AC: 64386 AN: 151996 Hom.: 14422 Cov.: 30 AF XY: 0.424 AC XY: 31475 AN XY: 74298

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.408

Alfa AF: 0.362 Hom.: 13449

Bravo AF: 0.439

Asia WGS AF: 0.479 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9402168; hg19: chr6-130066736;