chr2-59333279-T-C

Variant names:

• chr2-59333279-T-C
• rs2561893
• ENST00000412409.3:n.546-92176A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412409.3(ENSG00000233891):​n.546-92176A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,078 control chromosomes in the GnomAD database, including 8,151 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 0.32 (8151 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49
• Publications: 3 publications found

Genes affected

ENSG00000233891 (HGNC:):

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374754	XR_002959389.2	n.1447+54783A>G		intron_variant	Intron 1 of 3
LOC105374754	XR_940127.3	n.1617+51345A>G		intron_variant	Intron 2 of 4
LOC105374754	XR_940128.3	n.1617+51345A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233891	ENST00000412409.3	n.546-92176A>G		intron_variant	Intron 4 of 4	3
ENSG00000233891	ENST00000434611.1	n.99-10961A>G		intron_variant	Intron 1 of 3	3
ENSG00000233891	ENST00000440521.6	n.183+54783A>G		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48398 AN: 151958 Hom.: 8155 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.318 AC: 48412 AN: 152078 Hom.: 8151 Cov.: 32 AF XY: 0.323 AC XY: 24006 AN XY: 74344

African (AFR) AF: 0.220 AC: 9133 AN: 41526

American (AMR) AF: 0.447 AC: 6822 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2521 AN: 5160

South Asian (SAS) AF: 0.357 AC: 1721 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3271 AN: 10584

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22537 AN: 67936

Other (OTH) AF: 0.330 AC: 697 AN: 2114

Alfa AF: 0.298 Hom.: 2939

Bravo AF: 0.326

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	19
DANN	Benign	0.86
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2561893; hg19: chr2-59560414;