rs9399633

Variant names:

• chr6-148062948-T-C
• rs9399633

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 0.823 in 152,148 control chromosomes in the GnomAD database, including 51,916 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 0.82 (51916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 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: 0.823 AC: 125171 AN: 152028 Hom.: 51896 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.823 AC: 125243 AN: 152148 Hom.: 51916 Cov.: 32 AF XY: 0.819 AC XY: 60919 AN XY: 74368

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.808

Alfa AF: 0.841 Hom.: 12522

Bravo AF: 0.803

Asia WGS AF: 0.780 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9399633; hg19: chr6-148384084;