rs1136200

Positions:

• chr20-11810038-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000557899.2(LINC00687):​n.486C>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 ENST00000557899.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

Genes affected

LINC00687 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 16 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00687	NR_110635.1	n.473C>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00687	ENST00000427835.3	n.1117C>A		non_coding_transcript_exon_variant	6/6	3
LINC00687	ENST00000557899.2	n.486C>A		non_coding_transcript_exon_variant	2/2	2
LINC00687	ENST00000656506.1	n.603C>A		non_coding_transcript_exon_variant	3/3

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0223

Gnomad4 NFE exome AF: 0.0104

Gnomad4 OTH exome AF: 0.0417

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

Gnomad4 AFR AF: 0.00226

Gnomad4 AMR AF: 0.00771

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.0433

Gnomad4 SAS AF: 0.00600

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.00851

Alfa AF: 0.0144 Hom.: 2

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1136200; hg19: chr20-11790686;