13-22828854-T-C

Variant names:

• chr13-22828854-T-C
• rs2335347

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 0.209 in 152,018 control chromosomes in the GnomAD database, including 3,774 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 0.21 (3774 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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: 0.209 AC: 31729 AN: 151898 Hom.: 3773 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.209 AC: 31744 AN: 152018 Hom.: 3774 Cov.: 32 AF XY: 0.216 AC XY: 16035 AN XY: 74306

African (AFR) AF: 0.162 AC: 6718 AN: 41468

American (AMR) AF: 0.166 AC: 2529 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2654 AN: 5156

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4814

European-Finnish (FIN) AF: 0.320 AC: 3378 AN: 10562

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.207 AC: 14038 AN: 67972

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.203 Hom.: 1713

Bravo AF: 0.193

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	5.3
DANN	Benign	0.90
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs2335347; hg19: chr13-23402993;