21-16673220-T-C

Variant names:

• chr21-16673220-T-C
• rs2823960

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 0.463 in 151,636 control chromosomes in the GnomAD database, including 17,287 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 0.46 (17287 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.463 AC: 70136 AN: 151520 Hom.: 17281 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.463 AC: 70168 AN: 151636 Hom.: 17287 Cov.: 31 AF XY: 0.464 AC XY: 34398 AN XY: 74084

African (AFR) AF: 0.594 AC: 24577 AN: 41366

American (AMR) AF: 0.357 AC: 5432 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1635 AN: 3466

East Asian (EAS) AF: 0.759 AC: 3904 AN: 5144

South Asian (SAS) AF: 0.588 AC: 2831 AN: 4812

European-Finnish (FIN) AF: 0.332 AC: 3472 AN: 10460

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26614 AN: 67844

Other (OTH) AF: 0.457 AC: 960 AN: 2102

Alfa AF: 0.425 Hom.: 1789

Bravo AF: 0.466

Asia WGS AF: 0.628 AC: 2171 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.38
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2823960; hg19: chr21-18045539;