3-3580927-C-T

Variant names:

• chr3-3580927-C-T
• rs9829721
• ENST00000420000.6:n.200+45817G>A

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+45817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,098 control chromosomes in the GnomAD database, including 4,266 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 0.23 (4266 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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
ENSG00000223727	ENST00000420000.6	n.200+45817G>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34576 AN: 151980 Hom.: 4267 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.228 AC: 34606 AN: 152098 Hom.: 4266 Cov.: 32 AF XY: 0.225 AC XY: 16700 AN XY: 74356

African (AFR) AF: 0.341 AC: 14129 AN: 41458

American (AMR) AF: 0.202 AC: 3081 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3472

East Asian (EAS) AF: 0.139 AC: 718 AN: 5182

South Asian (SAS) AF: 0.126 AC: 605 AN: 4812

European-Finnish (FIN) AF: 0.167 AC: 1768 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12953 AN: 67992

Other (OTH) AF: 0.218 AC: 459 AN: 2110

Alfa AF: 0.188 Hom.: 2413

Bravo AF: 0.235

Asia WGS AF: 0.152 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.40
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9829721; hg19: chr3-3622611;