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:58936):

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

LOC105374754 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412409.3. 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
	ENSG00000233891	ENST00000412409.3	TSL:3	n.546-92176A>G		intron	N/A
	ENSG00000233891	ENST00000434611.1	TSL:3	n.99-10961A>G		intron	N/A
	ENSG00000233891	ENST00000440521.6	TSL:3	n.183+54783A>G		intron	N/A

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 v4.9

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;