rs2059849

Variant names:

• chr5-67315082-T-C
• rs2059849
• ENST00000824927.1:n.257+70420T>C

Variant summary

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

The ENST00000824927.1(ENSG00000307284):​n.257+70420T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,188 control chromosomes in the GnomAD database, including 7,524 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 0.24 (7524 hom., cov: 33)
• Consequence: ENSG00000307284 ENST00000824927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 3 publications found

Genes affected

ENSG00000307284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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
ENSG00000307284	ENST00000824927.1	n.257+70420T>C		intron_variant	Intron 2 of 2
ENSG00000307284	ENST00000824928.1	n.211+70420T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36725 AN: 152072 Hom.: 7494 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.0229

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.242 AC: 36804 AN: 152188 Hom.: 7524 Cov.: 33 AF XY: 0.232 AC XY: 17296 AN XY: 74420

African (AFR) AF: 0.560 AC: 23238 AN: 41468

American (AMR) AF: 0.142 AC: 2165 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0905 AC: 314 AN: 3470

East Asian (EAS) AF: 0.0229 AC: 119 AN: 5190

South Asian (SAS) AF: 0.0440 AC: 212 AN: 4822

European-Finnish (FIN) AF: 0.0876 AC: 930 AN: 10616

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9196 AN: 68014

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.158 Hom.: 11425

Bravo AF: 0.260

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2059849; hg19: chr5-66610910; COSMIC: COSV60150099;