rs1683614

Variant names:

• chr12-127586179-G-A
• rs1683614
• ENST00000660759.1:n.401-4463G>A

Variant summary

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

The ENST00000660759.1(ENSG00000286922):​n.401-4463G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,970 control chromosomes in the GnomAD database, including 4,824 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 0.24 (4824 hom., cov: 31)
• Consequence: ENSG00000286922 ENST00000660759.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 publications found

Genes affected

ENSG00000286922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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
ENSG00000286922	ENST00000660759.1	n.401-4463G>A		intron_variant	Intron 2 of 2
ENSG00000286922	ENST00000715414.1	n.502-13432G>A		intron_variant	Intron 5 of 5
ENSG00000286922	ENST00000715415.1	n.564+13074G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37054 AN: 151852 Hom.: 4818 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.244 AC: 37076 AN: 151970 Hom.: 4824 Cov.: 31 AF XY: 0.243 AC XY: 18019 AN XY: 74276

African (AFR) AF: 0.188 AC: 7813 AN: 41464

American (AMR) AF: 0.222 AC: 3387 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3466

East Asian (EAS) AF: 0.0412 AC: 212 AN: 5148

South Asian (SAS) AF: 0.206 AC: 990 AN: 4806

European-Finnish (FIN) AF: 0.304 AC: 3215 AN: 10562

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.289 AC: 19609 AN: 67946

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.274 Hom.: 20994

Bravo AF: 0.236

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1683614; hg19: chr12-128070724;