rs1146509

Variant names:

• chr1-94564025-G-T
• rs1146509
• ENST00000782778.1:n.341+412G>T

Variant summary

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

The ENST00000782778.1(ENSG00000301906):​n.341+412G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,928 control chromosomes in the GnomAD database, including 15,998 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 0.45 (15998 hom., cov: 32)
• Consequence: ENSG00000301906 ENST00000782778.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573
• Publications: 4 publications found

Genes affected

ENSG00000301906 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782778.1. 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
	ENSG00000301906	ENST00000782778.1		n.341+412G>T		intron	N/A
	ENSG00000301906	ENST00000782779.1		n.330+412G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67710 AN: 151810 Hom.: 15987 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.446 AC: 67753 AN: 151928 Hom.: 15998 Cov.: 32 AF XY: 0.445 AC XY: 33041 AN XY: 74234

African (AFR) AF: 0.288 AC: 11921 AN: 41422

American (AMR) AF: 0.508 AC: 7765 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1431 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2368 AN: 5156

South Asian (SAS) AF: 0.475 AC: 2288 AN: 4814

European-Finnish (FIN) AF: 0.498 AC: 5248 AN: 10534

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35024 AN: 67936

Other (OTH) AF: 0.484 AC: 1023 AN: 2112

Alfa AF: 0.486 Hom.: 14630

Bravo AF: 0.439

Asia WGS AF: 0.477 AC: 1659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.30
PhyloP100		0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1146509;

hg19: chr1-95029581;