rs9399840

Variant names:

• chr6-103628588-C-T
• rs9399840

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.505 AC: 20895 AN: 41406

American (AMR) AF: 0.534 AC: 8096 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1515 AN: 3456

East Asian (EAS) AF: 0.558 AC: 2869 AN: 5142

South Asian (SAS) AF: 0.687 AC: 3315 AN: 4826

European-Finnish (FIN) AF: 0.557 AC: 5893 AN: 10574

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.518 AC: 35137 AN: 67810

Other (OTH) AF: 0.511 AC: 1072 AN: 2098

Alfa AF: 0.518 Hom.: 32369

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9399840; hg19: chr6-104076463;