rs1411628

Variant names:

• chr13-111546974-G-A
• rs1411628

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 0.319 in 152,218 control chromosomes in the GnomAD database, including 9,177 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 0.32 (9177 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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: 0.319 AC: 48531 AN: 152100 Hom.: 9166 Cov.: 34

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.319 AC: 48555 AN: 152218 Hom.: 9177 Cov.: 34 AF XY: 0.324 AC XY: 24088 AN XY: 74412

African (AFR) AF: 0.103 AC: 4292 AN: 41544

American (AMR) AF: 0.352 AC: 5392 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1295 AN: 3470

East Asian (EAS) AF: 0.418 AC: 2165 AN: 5184

South Asian (SAS) AF: 0.357 AC: 1724 AN: 4824

European-Finnish (FIN) AF: 0.444 AC: 4696 AN: 10586

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

European-Non Finnish (NFE) AF: 0.409 AC: 27792 AN: 67990

Other (OTH) AF: 0.342 AC: 723 AN: 2116

Alfa AF: 0.377 Hom.: 36186

Bravo AF: 0.304

Asia WGS AF: 0.368 AC: 1278 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	0.37
DANN	Benign	0.40
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1411628; hg19: chr13-112199321;