chr21-17820455-G-T

Variant names:

• chr21-17820455-G-T
• rs10446073
• ENST00000813817.1:n.129+841G>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+841G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0642 in 152,208 control chromosomes in the GnomAD database, including 344 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 0.064 (344 hom., cov: 32)
• Consequence: ENSG00000305890 ENST00000813817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900465	XR_007067823.1	n.1605+63666G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305890	ENST00000813817.1	n.129+841G>T		intron_variant	Intron 1 of 1
ENSG00000305890	ENST00000813818.1	n.194+841G>T		intron_variant	Intron 1 of 1
ENSG00000305890	ENST00000813819.1	n.215-165G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9733 AN: 152090 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0564

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

GnomAD4 genome AF: 0.0642 AC: 9766 AN: 152208 Hom.: 344 Cov.: 32 AF XY: 0.0643 AC XY: 4788 AN XY: 74410

African (AFR) AF: 0.0856 AC: 3555 AN: 41542

American (AMR) AF: 0.0528 AC: 807 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3468

East Asian (EAS) AF: 0.0307 AC: 159 AN: 5178

South Asian (SAS) AF: 0.0564 AC: 272 AN: 4822

European-Finnish (FIN) AF: 0.0603 AC: 638 AN: 10580

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4060 AN: 68006

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0594 Hom.: 564

Bravo AF: 0.0646

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.80
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10446073; hg19: chr21-19192772;