21-19980221-C-T

Variant names:

• chr21-19980221-C-T
• rs385806
• XR_937603.2:n.359+6453C>T

Variant summary

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

The XR_937603.2(LOC105372745):​n.359+6453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,208 control chromosomes in the GnomAD database, including 61,005 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 0.89 (61005 hom., cov: 32)
• Consequence: LOC105372745 XR_937603.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 publications found

Genes affected

LOC105372745 (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 (AFR) allele frequency at 95% confidence interval = 0.941 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: 0.894 AC: 135980 AN: 152090 Hom.: 60954 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.894 AC: 136089 AN: 152208 Hom.: 61005 Cov.: 32 AF XY: 0.897 AC XY: 66713 AN XY: 74406

African (AFR) AF: 0.949 AC: 39412 AN: 41550

American (AMR) AF: 0.919 AC: 14042 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3097 AN: 3472

East Asian (EAS) AF: 0.929 AC: 4784 AN: 5152

South Asian (SAS) AF: 0.933 AC: 4504 AN: 4830

European-Finnish (FIN) AF: 0.893 AC: 9463 AN: 10594

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

European-Non Finnish (NFE) AF: 0.852 AC: 57944 AN: 68008

Other (OTH) AF: 0.890 AC: 1882 AN: 2114

Alfa AF: 0.877 Hom.: 22252

Bravo AF: 0.896

Asia WGS AF: 0.930 AC: 3233 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs385806; hg19: chr21-21352535;