21-45981279-G-T

Variant names:

• chr21-45981279-G-T
• rs17551710
• XR_937803.3:n.852-11G>T

Variant summary

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

The XR_937803.3(LOC105372841):​n.852-11G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,270 control chromosomes in the GnomAD database, including 3,367 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 0.16 (3367 hom., cov: 32)
• Consequence: LOC105372841 XR_937803.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 11 publications found

Genes affected

LOC105372841 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.163 AC: 24775 AN: 152152 Hom.: 3364 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0792

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.163 AC: 24801 AN: 152270 Hom.: 3367 Cov.: 32 AF XY: 0.159 AC XY: 11824 AN XY: 74472

African (AFR) AF: 0.369 AC: 15303 AN: 41510

American (AMR) AF: 0.103 AC: 1582 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0792 AC: 275 AN: 3472

East Asian (EAS) AF: 0.146 AC: 754 AN: 5170

South Asian (SAS) AF: 0.114 AC: 550 AN: 4832

European-Finnish (FIN) AF: 0.0438 AC: 465 AN: 10622

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0816 AC: 5548 AN: 68030

Other (OTH) AF: 0.131 AC: 278 AN: 2116

Alfa AF: 0.103 Hom.: 1946

Bravo AF: 0.175

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.59
PhyloP100		-1.0
PromoterAI		0.081	Neutral

Splicing

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

Other links and lift over

dbSNP: rs17551710; hg19: chr21-47401193;