21-45019979-C-T

Variant names:

• chr21-45019979-C-T
• rs7282671

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 0.192 in 152,270 control chromosomes in the GnomAD database, including 2,996 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 0.19 (2996 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29182 AN: 152152 Hom.: 2992 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.0687

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.192 AC: 29195 AN: 152270 Hom.: 2996 Cov.: 33 AF XY: 0.188 AC XY: 14017 AN XY: 74454

African (AFR) AF: 0.224 AC: 9289 AN: 41528

American (AMR) AF: 0.257 AC: 3930 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3472

East Asian (EAS) AF: 0.0360 AC: 187 AN: 5194

South Asian (SAS) AF: 0.0681 AC: 329 AN: 4830

European-Finnish (FIN) AF: 0.136 AC: 1448 AN: 10622

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12571 AN: 68016

Other (OTH) AF: 0.198 AC: 416 AN: 2104

Alfa AF: 0.179 Hom.: 3479

Bravo AF: 0.204

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7282671; hg19: chr21-46439894; COSMIC: COSV53455660;