chr12-3322405-C-A

Variant names:

• chr12-3322405-C-A
• rs1978238
• NR_187484.1:n.4487C>A

Variant summary

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

The NR_187484.1(LINC02827):​n.4487C>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 0.577 in 151,944 control chromosomes in the GnomAD database, including 25,716 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 0.58 (25716 hom., cov: 32)
• Consequence: LINC02827 NR_187484.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258
• Publications: 5 publications found

Genes affected

LINC02827 (HGNC:54358): (long intergenic non-protein coding RNA 2827)

ENSG00000250770 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02827	NR_187484.1	n.4487C>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC100128253	NR_148995.1	n.65-14587G>T		intron_variant	Intron 1 of 11
LINC02827	NR_187482.1	n.1609-944C>A		intron_variant	Intron 5 of 5
LINC02827	NR_187483.1	n.1982-944C>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02827	ENST00000432994.2	n.1010-944C>A		intron_variant	Intron 1 of 1	2
LINC02827	ENST00000543036.1	n.287-944C>A		intron_variant	Intron 1 of 2	2
ENSG00000250770	ENST00000635814.1	n.273+919G>T		intron_variant	Intron 2 of 6	6

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87621 AN: 151824 Hom.: 25698 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.552

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.577 AC: 87691 AN: 151944 Hom.: 25716 Cov.: 32 AF XY: 0.575 AC XY: 42734 AN XY: 74262

African (AFR) AF: 0.497 AC: 20579 AN: 41388

American (AMR) AF: 0.601 AC: 9180 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1916 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1701 AN: 5158

South Asian (SAS) AF: 0.650 AC: 3133 AN: 4822

European-Finnish (FIN) AF: 0.589 AC: 6215 AN: 10544

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43135 AN: 67972

Other (OTH) AF: 0.550 AC: 1158 AN: 2106

Alfa AF: 0.612 Hom.: 87979

Bravo AF: 0.572

Asia WGS AF: 0.513 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.28
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1978238; hg19: chr12-3431571;