21-33981573-G-T

Variant names:

• chr21-33981573-G-T
• rs2070513

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 0.379 in 151,926 control chromosomes in the GnomAD database, including 12,142 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 0.38 (12142 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

ACMG classification

Verdict is Benign. Variant got -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 = 0.567 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: 0.379 AC: 57535 AN: 151808 Hom.: 12117 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.379 AC: 57599 AN: 151926 Hom.: 12142 Cov.: 31 AF XY: 0.372 AC XY: 27622 AN XY: 74270

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.375

Alfa AF: 0.237 Hom.: 745

Bravo AF: 0.408

Asia WGS AF: 0.295 AC: 1028 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	0.019
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2070513; hg19: chr21-35353874;