rs9380350

Variant names:

• chr6-33159088-C-T
• rs9380350

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 0.143 in 140,746 control chromosomes in the GnomAD database, including 3,174 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 0.14 (3174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.143 AC: 20070 AN: 140636 Hom.: 3162 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.0523

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.143 AC: 20100 AN: 140746 Hom.: 3174 Cov.: 31 AF XY: 0.146 AC XY: 10029 AN XY: 68716

African (AFR) AF: 0.121 AC: 4801 AN: 39700

American (AMR) AF: 0.241 AC: 3268 AN: 13540

Ashkenazi Jewish (ASJ) AF: 0.0523 AC: 169 AN: 3234

East Asian (EAS) AF: 0.398 AC: 1645 AN: 4136

South Asian (SAS) AF: 0.0714 AC: 315 AN: 4410

European-Finnish (FIN) AF: 0.173 AC: 1686 AN: 9756

Middle Eastern (MID) AF: 0.108 AC: 27 AN: 250

European-Non Finnish (NFE) AF: 0.125 AC: 7848 AN: 62958

Other (OTH) AF: 0.149 AC: 282 AN: 1894

Alfa AF: 0.155 Hom.: 1108

Bravo AF: 0.205

Asia WGS AF: 0.216 AC: 738 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.25
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9380350; hg19: chr6-33126865;