rs2833017

Variant names:

• chr21-30714005-G-T
• rs2833017
• ENST00000731715.1:n.138-3300C>A

Variant summary

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

The ENST00000731715.1(ENSG00000295670):​n.138-3300C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,014 control chromosomes in the GnomAD database, including 24,850 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 0.57 (24850 hom., cov: 32)
• Consequence: ENSG00000295670 ENST00000731715.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 4 publications found

Genes affected

ENSG00000295670 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731715.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295670	ENST00000731715.1		n.138-3300C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86316 AN: 151896 Hom.: 24814 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.568 AC: 86403 AN: 152014 Hom.: 24850 Cov.: 32 AF XY: 0.564 AC XY: 41897 AN XY: 74286

African (AFR) AF: 0.569 AC: 23589 AN: 41460

American (AMR) AF: 0.636 AC: 9710 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1593 AN: 5172

South Asian (SAS) AF: 0.619 AC: 2984 AN: 4820

European-Finnish (FIN) AF: 0.493 AC: 5200 AN: 10548

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39130 AN: 67948

Other (OTH) AF: 0.607 AC: 1284 AN: 2116

Alfa AF: 0.579 Hom.: 14321

Bravo AF: 0.578

Asia WGS AF: 0.520 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.55
PhyloP100		0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2833017;

hg19: chr21-32086323;