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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724355	XR_430359.4	n.848-21060G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;