21-17834172-C-T

Variant names:

• chr21-17834172-C-T
• rs11088655
• ENST00000813817.1:n.129+14558C>T

Variant summary

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

The ENST00000813817.1(ENSG00000305890):​n.129+14558C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,992 control chromosomes in the GnomAD database, including 6,472 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 0.28 (6472 hom., cov: 33)
• Consequence: ENSG00000305890 ENST00000813817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

Genes affected

ENSG00000305890 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813817.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000305890	ENST00000813817.1		n.129+14558C>T		intron	N/A
	ENSG00000305890	ENST00000813818.1		n.194+14558C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41775 AN: 151874 Hom.: 6466 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.275 AC: 41810 AN: 151992 Hom.: 6472 Cov.: 33 AF XY: 0.276 AC XY: 20485 AN XY: 74310

African (AFR) AF: 0.406 AC: 16811 AN: 41456

American (AMR) AF: 0.191 AC: 2919 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3470

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5180

South Asian (SAS) AF: 0.186 AC: 898 AN: 4818

European-Finnish (FIN) AF: 0.330 AC: 3475 AN: 10542

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16011 AN: 67952

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.263 Hom.: 925

Bravo AF: 0.269

Asia WGS AF: 0.112 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.60
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11088655; hg19: chr21-19206489;