chr9-21081433-G-A

Variant names:

• chr9-21081433-G-A
• rs7033217

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 0.139 in 152,164 control chromosomes in the GnomAD database, including 1,765 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 (1765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 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: 0.139 AC: 21186 AN: 152046 Hom.: 1763 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.139 AC: 21178 AN: 152164 Hom.: 1765 Cov.: 32 AF XY: 0.137 AC XY: 10207 AN XY: 74402

African (AFR) AF: 0.0568 AC: 2359 AN: 41532

American (AMR) AF: 0.133 AC: 2024 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3468

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5182

South Asian (SAS) AF: 0.179 AC: 866 AN: 4830

European-Finnish (FIN) AF: 0.166 AC: 1761 AN: 10594

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12848 AN: 67980

Other (OTH) AF: 0.153 AC: 324 AN: 2112

Alfa AF: 0.143 Hom.: 261

Bravo AF: 0.132

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7033217; hg19: chr9-21081432;