chr21-27285630-C-T

Variant names:

• chr21-27285630-C-T
• rs457603
• XR_430359.4:n.848-21060G>A

Variant summary

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

The XR_430359.4(LOC102724355):​n.848-21060G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,146 control chromosomes in the GnomAD database, including 62,175 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 0.90 (62175 hom., cov: 30)
• Consequence: LOC102724355 XR_430359.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.904 AC: 137372 AN: 152028 Hom.: 62131 Cov.: 30

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.904 AC: 137472 AN: 152146 Hom.: 62175 Cov.: 30 AF XY: 0.906 AC XY: 67352 AN XY: 74372

African (AFR) AF: 0.914 AC: 37922 AN: 41498

American (AMR) AF: 0.886 AC: 13537 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3188 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5046 AN: 5166

South Asian (SAS) AF: 0.919 AC: 4427 AN: 4816

European-Finnish (FIN) AF: 0.937 AC: 9920 AN: 10584

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60480 AN: 68010

Other (OTH) AF: 0.895 AC: 1893 AN: 2114

Alfa AF: 0.894 Hom.: 84333

Bravo AF: 0.901

Asia WGS AF: 0.947 AC: 3290 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.60
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs457603; hg19: chr21-28657949;