rs3848459

Variant names:

• chr17-52827683-C-T
• rs3848459
• ENST00000791599.1:n.227+867G>A

Variant summary

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

The ENST00000791599.1(ENSG00000303078):​n.227+867G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 152,012 control chromosomes in the GnomAD database, including 1,121 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 0.079 (1121 hom., cov: 29)
• Consequence: ENSG00000303078 ENST00000791599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 0 publications found

Genes affected

ENSG00000303078 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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
ENSG00000303078	ENST00000791599.1	n.227+867G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11986 AN: 151894 Hom.: 1108 Cov.: 29

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0558

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

GnomAD4 genome AF: 0.0792 AC: 12032 AN: 152012 Hom.: 1121 Cov.: 29 AF XY: 0.0753 AC XY: 5599 AN XY: 74346

African (AFR) AF: 0.225 AC: 9298 AN: 41406

American (AMR) AF: 0.0396 AC: 604 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3466

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.0453 AC: 218 AN: 4810

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10602

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0235 AC: 1598 AN: 68004

Other (OTH) AF: 0.0552 AC: 116 AN: 2102

Alfa AF: 0.0671 Hom.: 153

Bravo AF: 0.0871

Asia WGS AF: 0.0400 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.29
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3848459; hg19: chr17-50905043;