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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000620459.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02967	ENST00000620459.2	TSL:6	n.1827A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301203	ENST00000776975.1		n.75+17424T>C		intron	N/A
	LINC02967	ENST00000777088.1		n.*32A>G		downstream_gene	N/A

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 v4.9

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;