rs227631

Variant names:

• chr20-24933017-A-G
• rs227631
• ENST00000620459.2:n.1827A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000620459.2(LINC02967):​n.1827A>G 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 0.217 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 ENST00000620459.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 4 publications found

Genes affected

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

ENSG00000301203 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02967	XR_001754563.2	n.*32A>G		downstream_gene_variant
LINC02967	XR_937399.3	n.*32A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02967	ENST00000620459.2	n.1827A>G		non_coding_transcript_exon_variant	Exon 2 of 2	6
ENSG00000301203	ENST00000776975.1	n.75+17424T>C		intron_variant	Intron 1 of 4
LINC02967	ENST00000777088.1	n.*32A>G		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

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: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.266 AC: 11024 AN: 41488

American (AMR) AF: 0.195 AC: 2977 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.0689 AC: 357 AN: 5178

South Asian (SAS) AF: 0.177 AC: 854 AN: 4820

European-Finnish (FIN) AF: 0.0862 AC: 913 AN: 10588

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15366 AN: 67986

Other (OTH) AF: 0.236 AC: 497 AN: 2104

Alfa AF: 0.202 Hom.: 433

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
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs227631; hg19: chr20-24913653;