ENST00000417800.1:n.101+82T>C

Variant names:

• chr6-137945548-T-C
• rs9321637
• ENST00000417800.1:n.101+82T>C

Variant summary

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

The ENST00000417800.1(LINC02865):​n.101+82T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,388 control chromosomes in the GnomAD database, including 2,777 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 0.17 (2776 hom., cov: 31)
  • Exomes 𝑓: 0.076 (1 hom.)
• Consequence: LINC02865 ENST00000417800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 14 publications found

Genes affected

LINC02865 (HGNC:54516): (long intergenic non-protein coding RNA 2865)

SIMALR (HGNC:53554): (suppressor of inflammatory macrophage apoptosis lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417800.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIMALR	NR_149097.1		n.132+121A>G		intron	N/A
	LINC02865	NR_174953.1		n.119+82T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02865	ENST00000417800.1	TSL:2	n.101+82T>C		intron	N/A
	SIMALR	ENST00000417932.2	TSL:3	n.355+121A>G		intron	N/A
	LINC02865	ENST00000434437.5	TSL:2	n.101+82T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25208 AN: 152086 Hom.: 2776 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.0761 AC: 14 AN: 184 Hom.: 1 Cov.: 0 AF XY: 0.0556 AC XY: 6 AN XY: 108

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0580 AC: 8 AN: 138

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.136 AC: 6 AN: 44

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.166 AC: 25221 AN: 152204 Hom.: 2776 Cov.: 31 AF XY: 0.162 AC XY: 12071 AN XY: 74412

African (AFR) AF: 0.316 AC: 13112 AN: 41492

American (AMR) AF: 0.0942 AC: 1442 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3470

East Asian (EAS) AF: 0.0235 AC: 122 AN: 5182

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4828

European-Finnish (FIN) AF: 0.123 AC: 1304 AN: 10616

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8055 AN: 67998

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.138 Hom.: 4119

Bravo AF: 0.168

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs9321637; hg19: chr6-138266685;