rs17781283

Variant names:

• chr6-137941636-G-A
• rs17781283
• ENST00000752757.1:n.167+9941G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000752757.1(LINC02865):​n.167+9941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,120 control chromosomes in the GnomAD database, including 47 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 0.020 (47 hom., cov: 33)
• Consequence: LINC02865 ENST00000752757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

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=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0204 (3102/152120) while in subpopulation NFE AF = 0.0311 (2116/67998). AF 95% confidence interval is 0.03. There are 47 homozygotes in GnomAd4. There are 1415 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02865	ENST00000752757.1	n.167+9941G>A		intron_variant	Intron 2 of 3
LINC02865	ENST00000752758.1	n.166-9505G>A		intron_variant	Intron 2 of 2
SIMALR	ENST00000752847.1	n.318-479C>T		intron_variant	Intron 3 of 3
SIMALR	ENST00000752848.1	n.297-479C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0204 AC: 3100 AN: 152002 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00570

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0127

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0311

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0204 AC: 3102 AN: 152120 Hom.: 47 Cov.: 33 AF XY: 0.0190 AC XY: 1415 AN XY: 74360

African (AFR) AF: 0.00569 AC: 236 AN: 41504

American (AMR) AF: 0.0219 AC: 334 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0131 AC: 63 AN: 4804

European-Finnish (FIN) AF: 0.0169 AC: 178 AN: 10562

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0311 AC: 2116 AN: 67998

Other (OTH) AF: 0.0185 AC: 39 AN: 2112

Alfa AF: 0.0247 Hom.: 31

Bravo AF: 0.0198

Asia WGS AF: 0.00462 AC: 16 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.68
DANN	Benign	0.47
PhyloP100		-0.54

Splicing

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

Publications

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Other links and lift over

dbSNP: rs17781283; hg19: chr6-138262773;