chr21-14661584-T-C

Variant names:

• chr21-14661584-T-C
• rs7280842

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 0.765 in 152,076 control chromosomes in the GnomAD database, including 45,337 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 0.77 (45337 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• 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 (NFE) allele frequency at 95% confidence interval = 0.828 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: 0.765 AC: 116307 AN: 151958 Hom.: 45316 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.765 AC: 116382 AN: 152076 Hom.: 45337 Cov.: 33 AF XY: 0.766 AC XY: 56900 AN XY: 74324

African (AFR) AF: 0.604 AC: 25050 AN: 41456

American (AMR) AF: 0.832 AC: 12684 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2817 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4205 AN: 5180

South Asian (SAS) AF: 0.728 AC: 3508 AN: 4818

European-Finnish (FIN) AF: 0.845 AC: 8946 AN: 10590

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56685 AN: 68004

Other (OTH) AF: 0.792 AC: 1676 AN: 2116

Alfa AF: 0.793 Hom.: 6790

Bravo AF: 0.759

Asia WGS AF: 0.776 AC: 2697 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	5.5
DANN	Benign	0.33
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7280842; hg19: chr21-16033905;