3-184655299-C-T

Variant names:

• chr3-184655299-C-T
• rs3890724
• ENST00000809115.1:n.184+3666G>A

Variant summary

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

The ENST00000809115.1(ENSG00000305160):​n.184+3666G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0606 in 152,146 control chromosomes in the GnomAD database, including 855 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 0.061 (855 hom., cov: 32)
• Consequence: ENSG00000305160 ENST00000809115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 0 publications found

Genes affected

ENSG00000305160 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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
ENSG00000305160	ENST00000809115.1	n.184+3666G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 9182 AN: 152028 Hom.: 850 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0230

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.00663

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00525

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0606 AC: 9218 AN: 152146 Hom.: 855 Cov.: 32 AF XY: 0.0580 AC XY: 4314 AN XY: 74400

African (AFR) AF: 0.201 AC: 8314 AN: 41448

American (AMR) AF: 0.0230 AC: 351 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3472

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5182

South Asian (SAS) AF: 0.00643 AC: 31 AN: 4820

European-Finnish (FIN) AF: 0.000566 AC: 6 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00525 AC: 357 AN: 68024

Other (OTH) AF: 0.0398 AC: 84 AN: 2112

Alfa AF: 0.00323 Hom.: 4

Bravo AF: 0.0692

Asia WGS AF: 0.0190 AC: 67 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3890724; hg19: chr3-184373087;