chr21-26781140-C-T

Variant names:

• chr21-26781140-C-T
• rs2830495

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 0.0704 in 152,128 control chromosomes in the GnomAD database, including 491 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 0.070 (491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 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: 0.0703 AC: 10693 AN: 152010 Hom.: 490 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0704 AC: 10711 AN: 152128 Hom.: 491 Cov.: 31 AF XY: 0.0678 AC XY: 5040 AN XY: 74376

African (AFR) AF: 0.119 AC: 4941 AN: 41450

American (AMR) AF: 0.0530 AC: 810 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3464

East Asian (EAS) AF: 0.0903 AC: 467 AN: 5170

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4824

European-Finnish (FIN) AF: 0.0248 AC: 263 AN: 10620

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0548 AC: 3725 AN: 67994

Other (OTH) AF: 0.0616 AC: 130 AN: 2110

Alfa AF: 0.0578 Hom.: 202

Bravo AF: 0.0737

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.50
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs2830495; hg19: chr21-28153459;