21-27293028-G-C

Variant names:

• chr21-27293028-G-C
• rs2830840
• XR_430359.4:n.848-28458C>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.848-28458C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,032 control chromosomes in the GnomAD database, including 24,275 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 0.55 (24275 hom., cov: 33)
• Consequence: LOC102724355 XR_430359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 11 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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 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: 0.547 AC: 83116 AN: 151914 Hom.: 24263 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.547 AC: 83151 AN: 152032 Hom.: 24275 Cov.: 33 AF XY: 0.546 AC XY: 40525 AN XY: 74280

African (AFR) AF: 0.353 AC: 14645 AN: 41486

American (AMR) AF: 0.488 AC: 7447 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2370 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3002 AN: 5156

South Asian (SAS) AF: 0.457 AC: 2199 AN: 4812

European-Finnish (FIN) AF: 0.656 AC: 6943 AN: 10576

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44503 AN: 67970

Other (OTH) AF: 0.577 AC: 1217 AN: 2110

Alfa AF: 0.625 Hom.: 15242

Bravo AF: 0.527

Asia WGS AF: 0.496 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	4.7
DANN	Benign	0.84
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs2830840; hg19: chr21-28665347;