rs1449866

Variant names:

• chr3-143157791-G-T
• rs1449866
• ENST00000840693.1:n.84-10534C>A

Variant summary

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

The ENST00000840693.1(ENSG00000309389):​n.84-10534C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,116 control chromosomes in the GnomAD database, including 3,768 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 0.20 (3768 hom., cov: 33)
• Consequence: ENSG00000309389 ENST00000840693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 4 publications found

Genes affected

ENSG00000309389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840693.1. 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
	ENSG00000309389	ENST00000840693.1		n.84-10534C>A		intron	N/A
	ENSG00000309389	ENST00000840694.1		n.65-3640C>A		intron	N/A
	ENSG00000309389	ENST00000840695.1		n.63-3501C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30440 AN: 151998 Hom.: 3757 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.200 AC: 30487 AN: 152116 Hom.: 3768 Cov.: 33 AF XY: 0.200 AC XY: 14875 AN XY: 74394

African (AFR) AF: 0.344 AC: 14276 AN: 41486

American (AMR) AF: 0.195 AC: 2971 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3468

East Asian (EAS) AF: 0.189 AC: 981 AN: 5184

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4818

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8725 AN: 67980

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.153 Hom.: 2104

Bravo AF: 0.214

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.71
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1449866; hg19: chr3-142876633;