rs4291789

Variant names:

• chr13-100020667-C-G
• rs4291789

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 0.25 in 152,126 control chromosomes in the GnomAD database, including 5,291 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 0.25 (5291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.250 AC: 37979 AN: 152006 Hom.: 5292 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0958

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.250 AC: 37986 AN: 152126 Hom.: 5291 Cov.: 32 AF XY: 0.246 AC XY: 18273 AN XY: 74344

African (AFR) AF: 0.139 AC: 5778 AN: 41516

American (AMR) AF: 0.262 AC: 3996 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5168

South Asian (SAS) AF: 0.0978 AC: 471 AN: 4818

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10574

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21493 AN: 67998

Other (OTH) AF: 0.295 AC: 620 AN: 2104

Alfa AF: 0.280 Hom.: 809

Bravo AF: 0.251

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.6
DANN	Benign	0.47
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4291789; hg19: chr13-100672921;