rs2838063

Variant names:

• chr21-41557202-A-C
• rs2838063
• XR_937738.1:n.1251+2095T>G

Variant summary

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

The XR_937738.1(LOC105372809):​n.1251+2095T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,182 control chromosomes in the GnomAD database, including 3,085 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 0.19 (3085 hom., cov: 33)
• Consequence: LOC105372809 XR_937738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.432
• Publications: 2 publications found

Genes affected

LOC105372809 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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: 0.192 AC: 29210 AN: 152064 Hom.: 3088 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.192 AC: 29212 AN: 152182 Hom.: 3085 Cov.: 33 AF XY: 0.191 AC XY: 14192 AN XY: 74406

African (AFR) AF: 0.117 AC: 4866 AN: 41518

American (AMR) AF: 0.212 AC: 3234 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.176 AC: 909 AN: 5178

South Asian (SAS) AF: 0.224 AC: 1080 AN: 4822

European-Finnish (FIN) AF: 0.196 AC: 2072 AN: 10596

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15451 AN: 67994

Other (OTH) AF: 0.204 AC: 430 AN: 2112

Alfa AF: 0.221 Hom.: 6053

Bravo AF: 0.192

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2838063; hg19: chr21-42929129;