rs17430279

Variant names:

• chr2-184571535-A-G
• rs17430279
• ENST00000820546.1:n.206-3549T>C

Variant summary

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

The ENST00000820546.1(ENSG00000283839):​n.206-3549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,056 control chromosomes in the GnomAD database, including 4,093 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 0.22 (4093 hom., cov: 32)
• Consequence: ENSG00000283839 ENST00000820546.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 9 publications found

Genes affected

ENSG00000283839 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 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
ENSG00000283839	ENST00000820546.1	n.206-3549T>C		intron_variant	Intron 2 of 2
ENSG00000283839	ENST00000820547.1	n.491-3549T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34142 AN: 151938 Hom.: 4087 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.225 AC: 34167 AN: 152056 Hom.: 4093 Cov.: 32 AF XY: 0.228 AC XY: 16940 AN XY: 74322

African (AFR) AF: 0.185 AC: 7680 AN: 41526

American (AMR) AF: 0.168 AC: 2567 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 823 AN: 3462

East Asian (EAS) AF: 0.169 AC: 873 AN: 5180

South Asian (SAS) AF: 0.374 AC: 1800 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3125 AN: 10538

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16465 AN: 67946

Other (OTH) AF: 0.229 AC: 482 AN: 2106

Alfa AF: 0.228 Hom.: 6230

Bravo AF: 0.208

Asia WGS AF: 0.263 AC: 912 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.68
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs17430279; hg19: chr2-185436262;