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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378861	XR_001738160.3	n.511+412G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301906	ENST00000782778.1	n.341+412G>T		intron_variant	Intron 1 of 2
ENSG00000301906	ENST00000782779.1	n.330+412G>T		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1146509; hg19: chr1-95029581;