rs528301

Variant names:

• chr2-44927769-G-A
• rs528301
• ENST00000432125.3:n.648-4190C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-44927769-G-A
• chr2-44927769-G-C
• chr2-44927769-G-T

Variant summary

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

The ENST00000432125.3(LINC01833):​n.648-4190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,178 control chromosomes in the GnomAD database, including 40,960 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 0.72 (40959 hom., cov: 34)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC01833 ENST00000432125.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 13 publications found

Genes affected

LINC01833 (HGNC:52644): (long intergenic non-protein coding RNA 1833)

ENSG00000278957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432125.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01833	NR_147195.1		n.378-4190C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01833	ENST00000432125.3	TSL:3	n.648-4190C>T		intron	N/A
	LINC01833	ENST00000437916.2	TSL:3	n.378-4190C>T		intron	N/A
	LINC01833	ENST00000760488.1		n.408-4190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109125 AN: 152058 Hom.: 40896 Cov.: 34

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.686

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.718 AC: 109250 AN: 152176 Hom.: 40959 Cov.: 34 AF XY: 0.725 AC XY: 53969 AN XY: 74390

African (AFR) AF: 0.915 AC: 37993 AN: 41542

American (AMR) AF: 0.754 AC: 11528 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5116 AN: 5196

South Asian (SAS) AF: 0.853 AC: 4122 AN: 4830

European-Finnish (FIN) AF: 0.646 AC: 6815 AN: 10552

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39110 AN: 67974

Other (OTH) AF: 0.689 AC: 1456 AN: 2114

Alfa AF: 0.633 Hom.: 75286

Bravo AF: 0.735

Asia WGS AF: 0.899 AC: 3123 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	14
DANN	Benign	0.69
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs528301; hg19: chr2-45154908;