rs9484823

Variant names:

• chr6-100213460-A-G
• rs9484823

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 0.18 in 152,054 control chromosomes in the GnomAD database, including 2,483 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 0.18 (2483 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.189 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: 0.180 AC: 27278 AN: 151934 Hom.: 2481 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 27314 AN: 152054 Hom.: 2483 Cov.: 32 AF XY: 0.180 AC XY: 13407 AN XY: 74338

African (AFR) AF: 0.190 AC: 7868 AN: 41476

American (AMR) AF: 0.195 AC: 2977 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3464

East Asian (EAS) AF: 0.135 AC: 697 AN: 5162

South Asian (SAS) AF: 0.183 AC: 881 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1855 AN: 10582

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11775 AN: 67986

Other (OTH) AF: 0.173 AC: 365 AN: 2106

Alfa AF: 0.179 Hom.: 8526

Bravo AF: 0.182

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.38
DANN	Benign	0.31
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs9484823; hg19: chr6-100661336; COSMIC: COSV69415798;