21-19472432-T-C

Variant names:

• chr21-19472432-T-C
• rs2825601

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 0.543 in 152,046 control chromosomes in the GnomAD database, including 25,173 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 0.54 (25173 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 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: 0.544 AC: 82612 AN: 151928 Hom.: 25173 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.543 AC: 82627 AN: 152046 Hom.: 25173 Cov.: 31 AF XY: 0.546 AC XY: 40563 AN XY: 74342

African (AFR) AF: 0.249 AC: 10331 AN: 41466

American (AMR) AF: 0.594 AC: 9077 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3468

East Asian (EAS) AF: 0.637 AC: 3288 AN: 5158

South Asian (SAS) AF: 0.604 AC: 2911 AN: 4816

European-Finnish (FIN) AF: 0.709 AC: 7495 AN: 10572

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45590 AN: 67976

Other (OTH) AF: 0.548 AC: 1159 AN: 2114

Alfa AF: 0.609 Hom.: 11289

Bravo AF: 0.527

Asia WGS AF: 0.561 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.63
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2825601; hg19: chr21-20844749;