ENST00000427835.3:n.1117C>A

Variant names:

• chr20-11810038-G-T
• rs1136200
• ENST00000427835.3:n.1117C>A

Variant summary

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

The ENST00000427835.3(LINC00687):​n.1117C>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 0.0109 in 152,918 control chromosomes in the GnomAD database, including 16 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 0.011 (16 hom., cov: 31)
  • Exomes 𝑓: 0.018 (0 hom.)
• Consequence: LINC00687 ENST00000427835.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 2 publications found

Genes affected

LINC00687 (HGNC:16194): (long intergenic non-protein coding RNA 687)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0108 (1650/152310) while in subpopulation EAS AF = 0.0433 (224/5176). AF 95% confidence interval is 0.0386. There are 16 homozygotes in GnomAd4. There are 829 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 16 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00687	NR_110635.1	n.473C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00687	ENST00000427835.3	n.1117C>A		non_coding_transcript_exon_variant	Exon 6 of 6	3
LINC00687	ENST00000557899.2	n.486C>A		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00687	ENST00000656506.1	n.603C>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0108 AC: 1648 AN: 152192 Hom.: 16 Cov.: 31

Gnomad AFR AF: 0.00227

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00766

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0432

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.00860

GnomAD4 exome AF: 0.0181 AC: 11 AN: 608 Hom.: 0 Cov.: 0 AF XY: 0.00872 AC XY: 3 AN XY: 344

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 8

European-Finnish (FIN) AF: 0.0223 AC: 8 AN: 358

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.0104 AC: 2 AN: 192

Other (OTH) AF: 0.0417 AC: 1 AN: 24

GnomAD4 genome AF: 0.0108 AC: 1650 AN: 152310 Hom.: 16 Cov.: 31 AF XY: 0.0111 AC XY: 829 AN XY: 74470

African (AFR) AF: 0.00226 AC: 94 AN: 41580

American (AMR) AF: 0.00771 AC: 118 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3468

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5176

South Asian (SAS) AF: 0.00600 AC: 29 AN: 4830

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 898 AN: 68022

Other (OTH) AF: 0.00851 AC: 18 AN: 2116

Alfa AF: 0.0135 Hom.: 7

Bravo AF: 0.00961

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.60
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1136200; hg19: chr20-11790686;