rs13383344

Variant names:

• chr2-240313231-A-G
• rs13383344

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 0.406 in 152,098 control chromosomes in the GnomAD database, including 13,200 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 0.41 (13200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.522 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: 0.406 AC: 61780 AN: 151982 Hom.: 13204 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.406 AC: 61786 AN: 152098 Hom.: 13200 Cov.: 33 AF XY: 0.412 AC XY: 30608 AN XY: 74364

African (AFR) AF: 0.266 AC: 11057 AN: 41500

American (AMR) AF: 0.532 AC: 8140 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3462

East Asian (EAS) AF: 0.462 AC: 2392 AN: 5174

South Asian (SAS) AF: 0.471 AC: 2267 AN: 4814

European-Finnish (FIN) AF: 0.434 AC: 4585 AN: 10574

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30272 AN: 67958

Other (OTH) AF: 0.430 AC: 908 AN: 2112

Alfa AF: 0.419 Hom.: 1734

Bravo AF: 0.411

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.2
DANN	Benign	0.87
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs13383344; hg19: chr2-241252648;