rs9302028

Variant names:

• chr13-94944177-C-A
• rs9302028

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 0.0488 in 152,092 control chromosomes in the GnomAD database, including 687 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 0.049 (687 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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: 0.0489 AC: 7427 AN: 151974 Hom.: 687 Cov.: 31

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0398

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

GnomAD4 genome AF: 0.0488 AC: 7424 AN: 152092 Hom.: 687 Cov.: 31 AF XY: 0.0530 AC XY: 3936 AN XY: 74334

African (AFR) AF: 0.0330 AC: 1370 AN: 41514

American (AMR) AF: 0.0263 AC: 402 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2407 AN: 5134

South Asian (SAS) AF: 0.0857 AC: 413 AN: 4818

European-Finnish (FIN) AF: 0.0673 AC: 712 AN: 10578

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0292 AC: 1988 AN: 68002

Other (OTH) AF: 0.0393 AC: 83 AN: 2110

Alfa AF: 0.0390 Hom.: 675

Bravo AF: 0.0466

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.72
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9302028; hg19: chr13-95596431;