21-23249105-T-C

Variant names:

• chr21-23249105-T-C
• rs2827991

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 0.355 in 151,592 control chromosomes in the GnomAD database, including 11,650 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 0.36 (11650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53836 AN: 151474 Hom.: 11652 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.355 AC: 53817 AN: 151592 Hom.: 11650 Cov.: 32 AF XY: 0.357 AC XY: 26407 AN XY: 74060

African (AFR) AF: 0.113 AC: 4681 AN: 41466

American (AMR) AF: 0.414 AC: 6288 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1701 AN: 3452

East Asian (EAS) AF: 0.229 AC: 1169 AN: 5104

South Asian (SAS) AF: 0.383 AC: 1842 AN: 4814

European-Finnish (FIN) AF: 0.488 AC: 5143 AN: 10534

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31610 AN: 67734

Other (OTH) AF: 0.353 AC: 745 AN: 2108

Alfa AF: 0.404 Hom.: 1697

Bravo AF: 0.341

Asia WGS AF: 0.291 AC: 1010 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.012
DANN	Benign	0.59
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2827991; hg19: chr21-24621427;