21-41672041-C-T

Variant names:

• chr21-41672041-C-T
• rs2838088
• XR_937742.2:n.549-28C>T

Variant summary

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

The XR_937742.2(LOC105372813):​n.549-28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,064 control chromosomes in the GnomAD database, including 3,334 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 0.21 (3334 hom., cov: 31)
• Consequence: LOC105372813 XR_937742.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617
• Publications: 5 publications found

Genes affected

LOC105372813 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 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: 0.207 AC: 31520 AN: 151946 Hom.: 3326 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.207 AC: 31551 AN: 152064 Hom.: 3334 Cov.: 31 AF XY: 0.209 AC XY: 15524 AN XY: 74340

African (AFR) AF: 0.203 AC: 8411 AN: 41478

American (AMR) AF: 0.194 AC: 2970 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1069 AN: 5150

South Asian (SAS) AF: 0.333 AC: 1604 AN: 4824

European-Finnish (FIN) AF: 0.200 AC: 2122 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14045 AN: 67952

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.222 Hom.: 10483

Bravo AF: 0.204

Asia WGS AF: 0.271 AC: 939 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	0.94
DANN	Benign	0.72
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2838088; hg19: chr21-43092201;