rs2823093

Variant names:

• chr21-15148511-G-A
• rs2823093
• ENST00000798068.1:n.161-6077G>A

Variant summary

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

The ENST00000798068.1(ENSG00000303916):​n.161-6077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,060 control chromosomes in the GnomAD database, including 7,959 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 0.31 (7959 hom., cov: 32)
• Consequence: ENSG00000303916 ENST00000798068.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 78 publications found

Genes affected

ENSG00000303916 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303916	ENST00000798068.1	n.161-6077G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 47024 AN: 151942 Hom.: 7930 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.310 AC: 47107 AN: 152060 Hom.: 7959 Cov.: 32 AF XY: 0.308 AC XY: 22862 AN XY: 74318

African (AFR) AF: 0.438 AC: 18174 AN: 41450

American (AMR) AF: 0.313 AC: 4785 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3468

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5176

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2489 AN: 10566

Middle Eastern (MID) AF: 0.288 AC: 83 AN: 288

European-Non Finnish (NFE) AF: 0.270 AC: 18345 AN: 67974

Other (OTH) AF: 0.293 AC: 618 AN: 2108

Alfa AF: 0.284 Hom.: 21328

Bravo AF: 0.320

Asia WGS AF: 0.191 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs2823093; hg19: chr21-16520832;