3-45226624-T-C

Variant names:

• chr3-45226624-T-C
• rs33751
• ENST00000816327.1:n.511+14098T>C

Variant summary

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

The ENST00000816327.1(ENSG00000306223):​n.511+14098T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,104 control chromosomes in the GnomAD database, including 46,528 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 0.76 (46528 hom., cov: 32)
• Consequence: ENSG00000306223 ENST00000816327.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 4 publications found

Genes affected

ENSG00000306223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816327.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306223	ENST00000816327.1		n.511+14098T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.757 AC: 114997 AN: 151990 Hom.: 46509 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.756 AC: 115057 AN: 152104 Hom.: 46528 Cov.: 32 AF XY: 0.765 AC XY: 56875 AN XY: 74354

African (AFR) AF: 0.442 AC: 18334 AN: 41498

American (AMR) AF: 0.858 AC: 13126 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2899 AN: 3468

East Asian (EAS) AF: 0.964 AC: 4951 AN: 5134

South Asian (SAS) AF: 0.886 AC: 4281 AN: 4830

European-Finnish (FIN) AF: 0.915 AC: 9688 AN: 10590

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59196 AN: 67966

Other (OTH) AF: 0.793 AC: 1676 AN: 2114

Alfa AF: 0.744 Hom.: 7614

Bravo AF: 0.733

Asia WGS AF: 0.909 AC: 3163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.35
PhyloP100		-2.3
PromoterAI		-0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs33751; hg19: chr3-45268116;