21-27324157-T-C

Variant names:

• chr21-27324157-T-C
• rs239713
• XR_430359.4:n.847+26342A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_430359.4(LOC102724355):​n.847+26342A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,202 control chromosomes in the GnomAD database, including 36,721 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 0.68 (36721 hom., cov: 34)
• Consequence: LOC102724355 XR_430359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 13 publications found

Genes affected

LOC102724355 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.682 AC: 103728 AN: 152084 Hom.: 36713 Cov.: 34

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.682 AC: 103775 AN: 152202 Hom.: 36721 Cov.: 34 AF XY: 0.686 AC XY: 51073 AN XY: 74418

African (AFR) AF: 0.480 AC: 19943 AN: 41508

American (AMR) AF: 0.721 AC: 11017 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4745 AN: 5166

South Asian (SAS) AF: 0.709 AC: 3425 AN: 4832

European-Finnish (FIN) AF: 0.828 AC: 8781 AN: 10602

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50816 AN: 68022

Other (OTH) AF: 0.697 AC: 1471 AN: 2110

Alfa AF: 0.730 Hom.: 187208

Bravo AF: 0.670

Asia WGS AF: 0.799 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs239713; hg19: chr21-28696476;