rs1403225

Variant names:

• chr4-170250744-A-G
• rs1403225
• ENST00000654867.2:n.237-22915A>G

Variant summary

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

The ENST00000654867.2(LINC01612):​n.237-22915A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,994 control chromosomes in the GnomAD database, including 9,140 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 0.33 (9140 hom., cov: 31)
• Consequence: LINC01612 ENST00000654867.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 1 publications found

Genes affected

LINC01612 (HGNC:51837): (long intergenic non-protein coding RNA 1612)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01612	NR_125889.1	n.193+23961A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01612	ENST00000654867.2	n.237-22915A>G		intron_variant	Intron 1 of 3
LINC01612	ENST00000657650.1	n.196+23961A>G		intron_variant	Intron 1 of 3
LINC01612	ENST00000665566.3	n.243+23961A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50399 AN: 151876 Hom.: 9138 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0179

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.332 AC: 50418 AN: 151994 Hom.: 9140 Cov.: 31 AF XY: 0.328 AC XY: 24396 AN XY: 74274

African (AFR) AF: 0.218 AC: 9048 AN: 41478

American (AMR) AF: 0.378 AC: 5763 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1253 AN: 3468

East Asian (EAS) AF: 0.0180 AC: 93 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3935 AN: 10562

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27906 AN: 67936

Other (OTH) AF: 0.333 AC: 702 AN: 2108

Alfa AF: 0.367 Hom.: 1402

Bravo AF: 0.327

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.6
DANN	Benign	0.65
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1403225; hg19: chr4-171171895;