rs2334946

chr13-22653921-T-C

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 0.383 in 152,040 control chromosomes in the GnomAD database, including 12,649 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 (12649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58101 AN: 151922 Hom.: 12623 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.383 AC: 58174 AN: 152040 Hom.: 12649 Cov.: 32 AF XY: 0.382 AC XY: 28432 AN XY: 74338

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.356

Alfa AF: 0.295 Hom.: 9272

Bravo AF: 0.383

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.68
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2334946; hg19: chr13-23228060;