rs9384167

Variant names:

• chr6-153953939-C-T
• rs9384167

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 0.178 in 152,046 control chromosomes in the GnomAD database, including 2,633 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 0.18 (2633 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 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: 0.178 AC: 27105 AN: 151928 Hom.: 2632 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.178 AC: 27106 AN: 152046 Hom.: 2633 Cov.: 32 AF XY: 0.187 AC XY: 13900 AN XY: 74318

African (AFR) AF: 0.105 AC: 4365 AN: 41482

American (AMR) AF: 0.249 AC: 3799 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1724 AN: 5162

South Asian (SAS) AF: 0.293 AC: 1409 AN: 4816

European-Finnish (FIN) AF: 0.231 AC: 2432 AN: 10550

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11956 AN: 67992

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.166 Hom.: 340

Bravo AF: 0.171

Asia WGS AF: 0.330 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.58
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs9384167; hg19: chr6-154275074;