13-22822187-G-T

Variant names:

• chr13-22822187-G-T
• rs1330919

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 0.537 in 151,976 control chromosomes in the GnomAD database, including 22,418 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 0.54 (22418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81536 AN: 151858 Hom.: 22396 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.537 AC: 81607 AN: 151976 Hom.: 22418 Cov.: 32 AF XY: 0.546 AC XY: 40524 AN XY: 74258

African (AFR) AF: 0.590 AC: 24447 AN: 41460

American (AMR) AF: 0.585 AC: 8939 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1758 AN: 3460

East Asian (EAS) AF: 0.798 AC: 4117 AN: 5158

South Asian (SAS) AF: 0.666 AC: 3200 AN: 4806

European-Finnish (FIN) AF: 0.522 AC: 5520 AN: 10566

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31996 AN: 67944

Other (OTH) AF: 0.517 AC: 1091 AN: 2110

Alfa AF: 0.499 Hom.: 80558

Bravo AF: 0.542

Asia WGS AF: 0.723 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs1330919; hg19: chr13-23396326;