ENST00000623092.1:n.2253G>A

Variant names:

• chr7-26540630-G-A
• rs1047022
• ENST00000623092.1:n.2253G>A

Variant summary

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

The ENST00000623092.1(ENSG00000280255):​n.2253G>A 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 0.133 in 152,094 control chromosomes in the GnomAD database, including 1,632 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 0.13 (1632 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000280255 ENST00000623092.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 4 publications found

Genes affected

ENSG00000280255 (HGNC:):

LINC02981 (HGNC:56055): (long intergenic non-protein coding RNA 2981)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623092.1. 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
	LINC02981	NR_148499.1		n.3763G>A		non_coding_transcript_exon	Exon 7 of 7
	LINC02981	NR_148500.1		n.3358G>A		non_coding_transcript_exon	Exon 6 of 6
	LINC02981	NR_148501.1		n.3641G>A		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280255	ENST00000623092.1	TSL:6	n.2253G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000301643	ENST00000780535.1		n.354-338G>A		intron	N/A
	ENSG00000301666	ENST00000780720.1		n.210-9143C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20201 AN: 151976 Hom.: 1630 Cov.: 33

Gnomad AFR AF: 0.0424

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0278

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.114

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: 0.133 AC: 20198 AN: 152094 Hom.: 1632 Cov.: 33 AF XY: 0.134 AC XY: 9980 AN XY: 74318

African (AFR) AF: 0.0423 AC: 1757 AN: 41514

American (AMR) AF: 0.0997 AC: 1525 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3468

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5176

South Asian (SAS) AF: 0.237 AC: 1138 AN: 4804

European-Finnish (FIN) AF: 0.207 AC: 2182 AN: 10550

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12414 AN: 67976

Other (OTH) AF: 0.113 AC: 238 AN: 2110

Alfa AF: 0.161 Hom.: 1126

Bravo AF: 0.118

Asia WGS AF: 0.110 AC: 382 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.0
DANN	Benign	0.55
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs1047022; hg19: chr7-26580249;