21-25630065-C-T

Variant names:

• chr21-25630065-C-T
• rs17001239

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 0.0912 in 152,276 control chromosomes in the GnomAD database, including 829 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 0.091 (829 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 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: 0.0912 AC: 13872 AN: 152158 Hom.: 821 Cov.: 32

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0881

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0912 AC: 13895 AN: 152276 Hom.: 829 Cov.: 32 AF XY: 0.0964 AC XY: 7176 AN XY: 74446

African (AFR) AF: 0.0580 AC: 2408 AN: 41548

American (AMR) AF: 0.115 AC: 1753 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0881 AC: 306 AN: 3472

East Asian (EAS) AF: 0.145 AC: 752 AN: 5178

South Asian (SAS) AF: 0.259 AC: 1249 AN: 4828

European-Finnish (FIN) AF: 0.0994 AC: 1055 AN: 10614

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0900 AC: 6118 AN: 68014

Other (OTH) AF: 0.0988 AC: 209 AN: 2116

Alfa AF: 0.0943 Hom.: 2214

Bravo AF: 0.0899

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs17001239; hg19: chr21-27002377;