21-42352323-A-G

Variant names:

• chr21-42352323-A-G
• rs225338
• XR_007067875.1:n.31A>G

Variant summary

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

The XR_007067875.1(LOC105372815):​n.31A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 146,378 control chromosomes in the GnomAD database, including 58,751 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 (58751 hom., cov: 21)
• Consequence: LOC105372815 XR_007067875.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 2 publications found

Genes affected

LOC105372815 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.896 AC: 131029 AN: 146264 Hom.: 58702 Cov.: 21

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.896 AC: 131136 AN: 146378 Hom.: 58751 Cov.: 21 AF XY: 0.891 AC XY: 63524 AN XY: 71270

African (AFR) AF: 0.931 AC: 36784 AN: 39510

American (AMR) AF: 0.847 AC: 12530 AN: 14800

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3165 AN: 3418

East Asian (EAS) AF: 0.654 AC: 3008 AN: 4598

South Asian (SAS) AF: 0.867 AC: 3921 AN: 4524

European-Finnish (FIN) AF: 0.838 AC: 8406 AN: 10028

Middle Eastern (MID) AF: 0.954 AC: 269 AN: 282

European-Non Finnish (NFE) AF: 0.911 AC: 60411 AN: 66286

Other (OTH) AF: 0.911 AC: 1865 AN: 2048

Alfa AF: 0.907 Hom.: 7609

Bravo AF: 0.897

Asia WGS AF: 0.742 AC: 2568 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs225338; hg19: chr21-43772432;