rs2828155

Variant names:

• chr21-23439462-C-A
• rs2828155
• ENST00000797133.1:n.644+30254C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-23439462-C-A
• chr21-23439462-C-T

Variant summary

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

The ENST00000797133.1(ENSG00000227716):​n.644+30254C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 149,580 control chromosomes in the GnomAD database, including 17,676 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 0.47 (17676 hom., cov: 30)
• Consequence: ENSG00000227716 ENST00000797133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 9 publications found

Genes affected

ENSG00000227716 (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 (SAS) allele frequency at 95% confidence interval = 0.573 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
ENSG00000227716	ENST00000797133.1	n.644+30254C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.472 AC: 70525 AN: 149492 Hom.: 17679 Cov.: 30

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.472 AC: 70532 AN: 149580 Hom.: 17676 Cov.: 30 AF XY: 0.473 AC XY: 34499 AN XY: 72896

African (AFR) AF: 0.298 AC: 12144 AN: 40798

American (AMR) AF: 0.417 AC: 6259 AN: 14996

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1985 AN: 3464

East Asian (EAS) AF: 0.422 AC: 2154 AN: 5108

South Asian (SAS) AF: 0.591 AC: 2833 AN: 4792

European-Finnish (FIN) AF: 0.551 AC: 5397 AN: 9796

Middle Eastern (MID) AF: 0.507 AC: 146 AN: 288

European-Non Finnish (NFE) AF: 0.565 AC: 38042 AN: 67336

Other (OTH) AF: 0.477 AC: 998 AN: 2092

Alfa AF: 0.507 Hom.: 10352

Bravo AF: 0.448

Asia WGS AF: 0.463 AC: 1601 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.29
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs2828155; hg19: chr21-24811782;