rs2828104

Variant names:

• chr21-23392431-C-A
• rs2828104
• ENST00000653972.1:n.1353-19347G>T

Your query was ambiguous. Multiple possible variants found:

• chr21-23392431-C-A
• chr21-23392431-C-G
• chr21-23392431-C-T

Variant summary

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

The ENST00000653972.1(ENSG00000228592):​n.1353-19347G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,876 control chromosomes in the GnomAD database, including 12,980 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 0.41 (12980 hom., cov: 32)
• Consequence: ENSG00000228592 ENST00000653972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 5 publications found

Genes affected

ENSG00000228592 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 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
ENSG00000228592	ENST00000653972.1	n.1353-19347G>T		intron_variant	Intron 2 of 5
ENSG00000228592	ENST00000656174.1	n.354-19347G>T		intron_variant	Intron 3 of 6
ENSG00000228592	ENST00000664912.1	n.144+11285G>T		intron_variant	Intron 1 of 4
ENSG00000228592	ENST00000665559.1	n.203-19347G>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62100 AN: 151758 Hom.: 12973 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.409 AC: 62122 AN: 151876 Hom.: 12980 Cov.: 32 AF XY: 0.411 AC XY: 30523 AN XY: 74198

African (AFR) AF: 0.341 AC: 14138 AN: 41410

American (AMR) AF: 0.400 AC: 6106 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2632 AN: 5128

South Asian (SAS) AF: 0.416 AC: 2007 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5126 AN: 10544

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29197 AN: 67930

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.413 Hom.: 21739

Bravo AF: 0.401

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.098
DANN	Benign	0.61
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2828104; hg19: chr21-24764752;