rs17529983

Variant names:

• chr11-60159566-G-A
• rs17529983
• ENST00000533106.2:n.550C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-60159566-G-A
• chr11-60159566-G-T

Variant summary

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

The ENST00000533106.2(LINC02705):​n.550C>T 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 0.306 in 151,348 control chromosomes in the GnomAD database, including 8,646 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 0.31 (8643 hom., cov: 31)
  • Exomes 𝑓: 0.35 (3 hom.)
• Consequence: LINC02705 ENST00000533106.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 11 publications found

Genes affected

LINC02705 (HGNC:54222): (long intergenic non-protein coding RNA 2705)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533106.2. 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
	LINC02705	ENST00000533106.2	TSL:3	n.550C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46251 AN: 151208 Hom.: 8645 Cov.: 31

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 3 AF XY: 0.350 AC XY: 7 AN XY: 20

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.389 AC: 7 AN: 18

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.306 AC: 46248 AN: 151322 Hom.: 8643 Cov.: 31 AF XY: 0.305 AC XY: 22549 AN XY: 73866

African (AFR) AF: 0.0970 AC: 3992 AN: 41158

American (AMR) AF: 0.299 AC: 4547 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1324 AN: 3464

East Asian (EAS) AF: 0.207 AC: 1068 AN: 5152

South Asian (SAS) AF: 0.515 AC: 2472 AN: 4798

European-Finnish (FIN) AF: 0.310 AC: 3223 AN: 10408

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28337 AN: 67844

Other (OTH) AF: 0.360 AC: 755 AN: 2098

Alfa AF: 0.338 Hom.: 1216

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17529983; hg19: chr11-59927039; COSMIC: COSV73298096;