rs11909487

Variant names:

• chr21-15690060-T-C
• rs11909487

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 0.386 in 151,928 control chromosomes in the GnomAD database, including 15,024 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 0.39 (15024 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 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: 0.385 AC: 58485 AN: 151808 Hom.: 14973 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.386 AC: 58596 AN: 151928 Hom.: 15024 Cov.: 32 AF XY: 0.384 AC XY: 28480 AN XY: 74262

African (AFR) AF: 0.738 AC: 30593 AN: 41472

American (AMR) AF: 0.274 AC: 4184 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1517 AN: 5138

South Asian (SAS) AF: 0.248 AC: 1192 AN: 4800

European-Finnish (FIN) AF: 0.299 AC: 3148 AN: 10530

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.237 AC: 16110 AN: 67938

Other (OTH) AF: 0.359 AC: 757 AN: 2108

Alfa AF: 0.305 Hom.: 18441

Bravo AF: 0.397

Asia WGS AF: 0.318 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.63
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11909487; hg19: chr21-17062379;