ENST00000641970.2:n.1207C>T

Variant names:

• chr5-25087616-G-A
• rs2047267
• ENST00000641970.2:n.1207C>T

Variant summary

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

The ENST00000641970.2(LINC02228):​n.1207C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.945 in 152,112 control chromosomes in the GnomAD database, including 68,519 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 0.95 (68519 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC02228 ENST00000641970.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 publications found

Genes affected

LINC02228 (HGNC:53097): (long intergenic non-protein coding RNA 2228)

LINC02211 (HGNC:53078): (long intergenic non-protein coding RNA 2211)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
LINC02228	ENST00000641970.2	n.1207C>T		non_coding_transcript_exon_variant	Exon 6 of 6
LINC02228	ENST00000726618.1	n.1087C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LINC02228	ENST00000726619.1	n.904C>T		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143744 AN: 151994 Hom.: 68497 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.981

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.956

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.945 AC: 143815 AN: 152112 Hom.: 68519 Cov.: 33 AF XY: 0.947 AC XY: 70463 AN XY: 74370

African (AFR) AF: 0.811 AC: 33650 AN: 41494

American (AMR) AF: 0.981 AC: 14985 AN: 15280

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5178

South Asian (SAS) AF: 0.999 AC: 4829 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10582 AN: 10584

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67902 AN: 67952

Other (OTH) AF: 0.956 AC: 2022 AN: 2116

Alfa AF: 0.966 Hom.: 9214

Bravo AF: 0.939

Asia WGS AF: 0.988 AC: 3416 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.058
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2047267; hg19: chr5-25087725;