rs17380639

chr3-156775056-C-T

Variant summary

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

The NR_038387.1(LINC00886):n.177-23873G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0319 in 152,230 control chromosomes in the GnomAD database, including 113 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 0.032 (113 hom., cov: 32)
• Consequence: LINC00886 NR_038387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

LINC00886 (HGNC:48572): (long intergenic non-protein coding RNA 886)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0319 (4863/152230) while in subpopulation NFE AF= 0.0475 (3233/68022). AF 95% confidence interval is 0.0462. There are 113 homozygotes in gnomad4. There are 2380 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 113 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00886	NR_038387.1	n.177-23873G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00886	ENST00000472943.5	n.149-23873G>A		intron_variant, non_coding_transcript_variant		2
LINC00886	ENST00000473352.1	n.177-21604G>A		intron_variant, non_coding_transcript_variant		4
LINC00886	ENST00000664482.1	n.128-23873G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4865 AN: 152112 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00867

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00601

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0319 AC: 4863 AN: 152230 Hom.: 113 Cov.: 32 AF XY: 0.0320 AC XY: 2380 AN XY: 74434

Gnomad4 AFR AF: 0.00864

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0300

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0747

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0175

Alfa AF: 0.0426 Hom.: 174

Bravo AF: 0.0271

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17380639; hg19: chr3-156492845;