rs9348153

Variant names:

• chr6-158222494-C-T
• rs9348153

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 0.163 in 152,016 control chromosomes in the GnomAD database, including 2,828 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 0.16 (2828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.162 AC: 24649 AN: 151898 Hom.: 2807 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.163 AC: 24725 AN: 152016 Hom.: 2828 Cov.: 32 AF XY: 0.166 AC XY: 12334 AN XY: 74290

African (AFR) AF: 0.240 AC: 9945 AN: 41452

American (AMR) AF: 0.307 AC: 4681 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 213 AN: 3456

East Asian (EAS) AF: 0.415 AC: 2144 AN: 5170

South Asian (SAS) AF: 0.165 AC: 796 AN: 4820

European-Finnish (FIN) AF: 0.0812 AC: 859 AN: 10578

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5682 AN: 67968

Other (OTH) AF: 0.154 AC: 325 AN: 2110

Alfa AF: 0.114 Hom.: 5677

Bravo AF: 0.185

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.8
DANN	Benign	0.85
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9348153; hg19: chr6-158643526;