rs9399840

chr6-103628588-C-T

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 0.523 in 151,682 control chromosomes in the GnomAD database, including 20,870 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 0.52 (20870 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79246 AN: 151562 Hom.: 20851 Cov.: 33

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.523 AC: 79313 AN: 151682 Hom.: 20870 Cov.: 33 AF XY: 0.528 AC XY: 39166 AN XY: 74140

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.511

Alfa AF: 0.516 Hom.: 24250

Bravo AF: 0.514

Asia WGS AF: 0.664 AC: 2300 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.016
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9399840; hg19: chr6-104076463;