rs9369421

Variant names:

• chr6-43794385-T-C
• rs9369421

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 0.135 in 152,220 control chromosomes in the GnomAD database, including 1,809 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 0.13 (1809 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 8 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 (AFR) allele frequency at 95% confidence interval = 0.244 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: 0.135 AC: 20523 AN: 152102 Hom.: 1805 Cov.: 33

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.135 AC: 20541 AN: 152220 Hom.: 1809 Cov.: 33 AF XY: 0.135 AC XY: 10044 AN XY: 74440

African (AFR) AF: 0.248 AC: 10294 AN: 41504

American (AMR) AF: 0.0881 AC: 1347 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1050 AN: 5170

South Asian (SAS) AF: 0.146 AC: 704 AN: 4834

European-Finnish (FIN) AF: 0.0831 AC: 881 AN: 10608

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0822 AC: 5592 AN: 68018

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.0926 Hom.: 1603

Bravo AF: 0.140

Asia WGS AF: 0.185 AC: 646 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	0.95
DANN	Benign	0.47
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs9369421; hg19: chr6-43762122;