13-22828854-T-C

Variant names:

• chr13-22828854-T-C
• rs2335347

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.209 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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.187

Alfa AF: 0.204 Hom.: 1570

Bravo AF: 0.193

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2335347; hg19: chr13-23402993;