4-13008363-A-G

Variant names:

• chr4-13008363-A-G
• rs2056116

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.344 in 152,002 control chromosomes in the GnomAD database, including 9,289 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 0.34 (9289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.74
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 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: 0.344 AC: 52281 AN: 151884 Hom.: 9281 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.344 AC: 52299 AN: 152002 Hom.: 9289 Cov.: 32 AF XY: 0.343 AC XY: 25490 AN XY: 74284

African (AFR) AF: 0.290 AC: 12024 AN: 41468

American (AMR) AF: 0.287 AC: 4379 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1498 AN: 5168

South Asian (SAS) AF: 0.439 AC: 2113 AN: 4812

European-Finnish (FIN) AF: 0.362 AC: 3822 AN: 10546

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26379 AN: 67946

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.367 Hom.: 41979

Bravo AF: 0.332

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs2056116; hg19: chr4-13009987;