rs227631

Positions:

• chr20-24933017-A-G
• chr20-24933017-A-T

Variant summary

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

The 20-24933017-A-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,120 control chromosomes in the GnomAD database, including 3,848 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 0.22 (3848 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02967 ENST00000620459.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88

Genes affected

LINC02967 (HGNC:56007): (long intergenic non-protein coding RNA 2967)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02967	XR_001754563.2			downstream_gene_variant
LINC02967	XR_937399.3			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02967	ENST00000620459.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32933 AN: 152002 Hom.: 3845 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.236

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.217 AC: 32964 AN: 152120 Hom.: 3848 Cov.: 33 AF XY: 0.209 AC XY: 15534 AN XY: 74374

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0689

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0862

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.236

Alfa AF: 0.200 Hom.: 408

Bravo AF: 0.225

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227631; hg19: chr20-24913653;