rs280943

Variant names:

• chr13-29620694-G-A
• rs280943

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 0.373 in 151,948 control chromosomes in the GnomAD database, including 10,949 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 0.37 (10949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56575 AN: 151830 Hom.: 10932 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.373 AC: 56606 AN: 151948 Hom.: 10949 Cov.: 32 AF XY: 0.377 AC XY: 28003 AN XY: 74262

African (AFR) AF: 0.303 AC: 12562 AN: 41454

American (AMR) AF: 0.466 AC: 7107 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1749 AN: 5174

South Asian (SAS) AF: 0.465 AC: 2237 AN: 4812

European-Finnish (FIN) AF: 0.400 AC: 4207 AN: 10530

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 25997 AN: 67942

Other (OTH) AF: 0.399 AC: 838 AN: 2102

Alfa AF: 0.380 Hom.: 1499

Bravo AF: 0.374

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs280943; hg19: chr13-30194831;