rs13050102

Variant names:

• chr21-31870212-C-T
• rs13050102

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 0.334 in 152,044 control chromosomes in the GnomAD database, including 9,278 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 0.33 (9278 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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: 0.334 AC: 50745 AN: 151926 Hom.: 9269 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.346

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.334 AC: 50772 AN: 152044 Hom.: 9278 Cov.: 33 AF XY: 0.332 AC XY: 24670 AN XY: 74332

African (AFR) AF: 0.203 AC: 8421 AN: 41450

American (AMR) AF: 0.299 AC: 4564 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1298 AN: 5180

South Asian (SAS) AF: 0.314 AC: 1512 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4219 AN: 10552

Middle Eastern (MID) AF: 0.341 AC: 99 AN: 290

European-Non Finnish (NFE) AF: 0.416 AC: 28312 AN: 67976

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.390 Hom.: 6163

Bravo AF: 0.323

Asia WGS AF: 0.265 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	4.5
DANN	Benign	0.86
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs13050102; hg19: chr21-33242525;