17-5733334-C-G

Variant names:

• chr17-5733334-C-G
• rs12450571
• ENST00000783338.1:n.187-32789G>C

Variant summary

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

The ENST00000783338.1(ENSG00000286356):​n.187-32789G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,014 control chromosomes in the GnomAD database, including 14,846 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 0.44 (14846 hom., cov: 32)
• Consequence: ENSG00000286356 ENST00000783338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 publications found

Genes affected

ENSG00000286356 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783338.1. 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
	ENSG00000286356	ENST00000783338.1		n.187-32789G>C		intron	N/A
	ENSG00000286356	ENST00000783339.1		n.174-13989G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66900 AN: 151894 Hom.: 14835 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.440 AC: 66941 AN: 152014 Hom.: 14846 Cov.: 32 AF XY: 0.437 AC XY: 32481 AN XY: 74280

African (AFR) AF: 0.418 AC: 17337 AN: 41472

American (AMR) AF: 0.497 AC: 7603 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1475 AN: 5170

South Asian (SAS) AF: 0.430 AC: 2070 AN: 4816

European-Finnish (FIN) AF: 0.398 AC: 4200 AN: 10552

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31033 AN: 67942

Other (OTH) AF: 0.468 AC: 987 AN: 2110

Alfa AF: 0.284 Hom.: 650

Bravo AF: 0.447

Asia WGS AF: 0.386 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs12450571; hg19: chr17-5636654; COSMIC: COSV73905376;