chr21-13514758-A-G

Variant names:

• chr21-13514758-A-G
• rs11088680

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 0.308 in 151,234 control chromosomes in the GnomAD database, including 9,026 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 0.31 (9026 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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: 0.307 AC: 46459 AN: 151116 Hom.: 9015 Cov.: 30

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.308 AC: 46508 AN: 151234 Hom.: 9026 Cov.: 30 AF XY: 0.311 AC XY: 22996 AN XY: 73890

African (AFR) AF: 0.451 AC: 18559 AN: 41138

American (AMR) AF: 0.262 AC: 3980 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3468

East Asian (EAS) AF: 0.882 AC: 4399 AN: 4986

South Asian (SAS) AF: 0.384 AC: 1827 AN: 4756

European-Finnish (FIN) AF: 0.216 AC: 2278 AN: 10568

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13676 AN: 67810

Other (OTH) AF: 0.319 AC: 671 AN: 2102

Alfa AF: 0.252 Hom.: 711

Bravo AF: 0.323

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.28
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11088680; hg19: chr21-14887079;