rs450433

Variant names:

• chr17-74006384-G-A
• rs450433
• ENST00000727414.1:n.558+7226C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-74006384-G-A
• chr17-74006384-G-C
• chr17-74006384-G-T

Variant summary

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

The ENST00000727414.1(ENSG00000285648):​n.558+7226C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,926 control chromosomes in the GnomAD database, including 19,828 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 0.51 (19828 hom., cov: 31)
• Consequence: ENSG00000285648 ENST00000727414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.974
• Publications: 4 publications found

Genes affected

ENSG00000285648 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727414.1. 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
	ENSG00000285648	ENST00000727414.1		n.558+7226C>T		intron	N/A
	ENSG00000285648	ENST00000727417.1		n.480-7190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77131 AN: 151808 Hom.: 19810 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.508 AC: 77179 AN: 151926 Hom.: 19828 Cov.: 31 AF XY: 0.505 AC XY: 37453 AN XY: 74228

African (AFR) AF: 0.486 AC: 20136 AN: 41420

American (AMR) AF: 0.583 AC: 8909 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3468

East Asian (EAS) AF: 0.516 AC: 2653 AN: 5146

South Asian (SAS) AF: 0.410 AC: 1969 AN: 4800

European-Finnish (FIN) AF: 0.439 AC: 4637 AN: 10562

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35209 AN: 67938

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.514 Hom.: 77607

Bravo AF: 0.522

Asia WGS AF: 0.453 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.17
DANN	Benign	0.73
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs450433; hg19: chr17-72002523;