rs11661856

Variant names:

• chr18-77941567-G-A
• rs11661856
• ENST00000819455.1:n.93-16830C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-77941567-G-A
• chr18-77941567-G-T

Variant summary

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

The ENST00000819455.1(LINC01029):​n.93-16830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0326 in 151,088 control chromosomes in the GnomAD database, including 114 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 0.033 (114 hom., cov: 32)
• Consequence: LINC01029 ENST00000819455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 8 publications found

Genes affected

LINC01029 (HGNC:49015): (long intergenic non-protein coding RNA 1029)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0326 (4930/151088) while in subpopulation NFE AF = 0.0487 (3298/67780). AF 95% confidence interval is 0.0473. There are 114 homozygotes in GnomAd4. There are 2337 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 114 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
LINC01029	ENST00000819455.1	n.93-16830C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4931 AN: 150970 Hom.: 114 Cov.: 32

Gnomad AFR AF: 0.00971

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00588

Gnomad FIN AF: 0.0388

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0487

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0326 AC: 4930 AN: 151088 Hom.: 114 Cov.: 32 AF XY: 0.0317 AC XY: 2337 AN XY: 73744

African (AFR) AF: 0.00968 AC: 398 AN: 41108

American (AMR) AF: 0.0322 AC: 489 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3464

East Asian (EAS) AF: 0.000195 AC: 1 AN: 5138

South Asian (SAS) AF: 0.00588 AC: 28 AN: 4758

European-Finnish (FIN) AF: 0.0388 AC: 403 AN: 10380

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0487 AC: 3298 AN: 67780

Other (OTH) AF: 0.0426 AC: 89 AN: 2090

Alfa AF: 0.0400 Hom.: 247

Bravo AF: 0.0313

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.95
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11661856; hg19: chr18-75653523;