rs13340713

Positions:

• chr9-21220122-C-G
• chr9-21220122-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 142 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0518

Gnomad4 AMR AF: 0.0359

Gnomad4 ASJ AF: 0.0405

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00937

Gnomad4 FIN AF: 0.0160

Gnomad4 NFE AF: 0.0459

Gnomad4 OTH AF: 0.0477

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13340713; hg19: chr9-21220121;