chr9-88645647-C-T

Variant names:

• chr9-88645647-C-T
• rs17054265
• ENST00000544644.2:n.795+1274G>A

Variant summary

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

The ENST00000544644.2(LINC02843):​n.795+1274G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,024 control chromosomes in the GnomAD database, including 6,943 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 0.28 (6943 hom., cov: 32)
• Consequence: LINC02843 ENST00000544644.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 2 publications found

Genes affected

LINC02843 (HGNC:27847): (long intergenic non-protein coding RNA 2843)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02843	NR_144626.1	n.940+1274G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02843	ENST00000544644.2	n.795+1274G>A		intron_variant	Intron 3 of 4	1
LINC02843	ENST00000657830.1	n.2234G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC02843	ENST00000418343.3	n.953+1274G>A		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42881 AN: 151906 Hom.: 6930 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.282 AC: 42933 AN: 152024 Hom.: 6943 Cov.: 32 AF XY: 0.275 AC XY: 20468 AN XY: 74322

African (AFR) AF: 0.427 AC: 17705 AN: 41426

American (AMR) AF: 0.207 AC: 3162 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3466

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5164

South Asian (SAS) AF: 0.231 AC: 1109 AN: 4810

European-Finnish (FIN) AF: 0.182 AC: 1921 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16927 AN: 67996

Other (OTH) AF: 0.261 AC: 552 AN: 2116

Alfa AF: 0.256 Hom.: 19805

Bravo AF: 0.291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs17054265; hg19: chr9-91260562;