21-31669690-T-G

Variant names:

• chr21-31669690-T-G
• rs17880135

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0393 in 152,326 control chromosomes in the GnomAD database, including 161 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 0.039 (161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0582 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: 0.0393 AC: 5982 AN: 152208 Hom.: 161 Cov.: 33

Gnomad AFR AF: 0.0108

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0393 AC: 5981 AN: 152326 Hom.: 161 Cov.: 33 AF XY: 0.0385 AC XY: 2867 AN XY: 74502

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0382

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0598

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0456 Hom.: 74

Bravo AF: 0.0355

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.85
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17880135; hg19: chr21-33042003;