chr13-22838784-G-A

Variant names:

• chr13-22838784-G-A
• rs9552733

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 0.375 in 151,968 control chromosomes in the GnomAD database, including 11,426 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 0.38 (11426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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: 0.375 AC: 56988 AN: 151850 Hom.: 11427 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.375 AC: 57012 AN: 151968 Hom.: 11426 Cov.: 32 AF XY: 0.377 AC XY: 27965 AN XY: 74262

African (AFR) AF: 0.245 AC: 10161 AN: 41440

American (AMR) AF: 0.310 AC: 4731 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3464

East Asian (EAS) AF: 0.516 AC: 2667 AN: 5172

South Asian (SAS) AF: 0.370 AC: 1780 AN: 4810

European-Finnish (FIN) AF: 0.486 AC: 5118 AN: 10538

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30126 AN: 67950

Other (OTH) AF: 0.382 AC: 806 AN: 2112

Alfa AF: 0.395 Hom.: 11831

Bravo AF: 0.355

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs9552733; hg19: chr13-23412923; COSMIC: COSV69964152;