rs830407

Variant names:

• chr9-33217268-G-A
• rs830407

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 0.244 in 152,062 control chromosomes in the GnomAD database, including 7,618 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 0.24 (7618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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: 0.244 AC: 37102 AN: 151944 Hom.: 7592 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.244 AC: 37177 AN: 152062 Hom.: 7618 Cov.: 32 AF XY: 0.240 AC XY: 17830 AN XY: 74332

African (AFR) AF: 0.567 AC: 23482 AN: 41446

American (AMR) AF: 0.142 AC: 2171 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3470

East Asian (EAS) AF: 0.139 AC: 720 AN: 5182

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1297 AN: 10582

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7570 AN: 67970

Other (OTH) AF: 0.217 AC: 458 AN: 2106

Alfa AF: 0.305 Hom.: 4603

Bravo AF: 0.257

Asia WGS AF: 0.216 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.56
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs830407; hg19: chr9-33217266;