9-21220122-C-G

Variant names:

• chr9-21220122-C-G
• rs13340713

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0415 in 151,436 control chromosomes in the GnomAD database, including 142 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 0.042 (142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0415 (6286/151436) while in subpopulation AFR AF = 0.0518 (2141/41330). AF 95% confidence interval is 0.05. There are 142 homozygotes in GnomAd4. There are 2931 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 142 gene

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: 0.0414 AC: 6269 AN: 151318 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0405

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00936

Gnomad FIN AF: 0.0160

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0415 AC: 6286 AN: 151436 Hom.: 142 Cov.: 32 AF XY: 0.0396 AC XY: 2931 AN XY: 74030

African (AFR) AF: 0.0518 AC: 2141 AN: 41330

American (AMR) AF: 0.0359 AC: 544 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.0405 AC: 140 AN: 3458

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.00937 AC: 45 AN: 4802

European-Finnish (FIN) AF: 0.0160 AC: 169 AN: 10550

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0459 AC: 3108 AN: 67692

Other (OTH) AF: 0.0477 AC: 100 AN: 2098

Alfa AF: 0.00698 Hom.: 2

Bravo AF: 0.0446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.37
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs13340713; hg19: chr9-21220121;