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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372745	XR_937603.2	n.359+6453C>T		intron_variant	Intron 3 of 3

Ensembl

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

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 v4.3

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;