chr21-26691487-A-T

Variant names:

• chr21-26691487-A-T
• rs2830395

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 0.381 in 152,090 control chromosomes in the GnomAD database, including 11,971 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 (11971 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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: 0.381 AC: 57925 AN: 151970 Hom.: 11974 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.381 AC: 57939 AN: 152090 Hom.: 11971 Cov.: 33 AF XY: 0.384 AC XY: 28521 AN XY: 74364

African (AFR) AF: 0.223 AC: 9257 AN: 41498

American (AMR) AF: 0.386 AC: 5895 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3466

East Asian (EAS) AF: 0.248 AC: 1279 AN: 5166

South Asian (SAS) AF: 0.353 AC: 1704 AN: 4826

European-Finnish (FIN) AF: 0.529 AC: 5595 AN: 10572

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31197 AN: 67966

Other (OTH) AF: 0.398 AC: 838 AN: 2106

Alfa AF: 0.415 Hom.: 1664

Bravo AF: 0.369

Asia WGS AF: 0.309 AC: 1072 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.68
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs2830395; hg19: chr21-28063806;