rs1047022

Positions:

• chr7-26540630-G-A
• chr7-26540630-G-C
• chr7-26540630-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_148499.1(LINC02981):​n.3763G>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: LINC02981 NR_148499.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02981	NR_148499.1	n.3763G>A		non_coding_transcript_exon_variant	7/7
LINC02981	NR_148500.1	n.3358G>A		non_coding_transcript_exon_variant	6/6
LINC02981	NR_148501.1	n.3641G>A		non_coding_transcript_exon_variant	6/6
LINC02981	NR_148502.1	n.3586G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000623092.1	n.2253G>A		non_coding_transcript_exon_variant	1/1

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

GnomAD4 genome AF: 0.133 AC: 20198 AN: 152094 Hom.: 1632 Cov.: 33 AF XY: 0.134 AC XY: 9980 AN XY: 74318

Gnomad4 AFR AF: 0.0423

Gnomad4 AMR AF: 0.0997

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.113

Alfa AF: 0.162 Hom.: 1001

Bravo AF: 0.118

Asia WGS AF: 0.110 AC: 382 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1047022; hg19: chr7-26580249;