3-157232790-C-T

Variant names:

• chr3-157232790-C-T
• rs9866141
• ENST00000460796.2:n.168-6800C>T

Variant summary

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

The ENST00000460796.2(LINC00881):​n.168-6800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 152,124 control chromosomes in the GnomAD database, including 234 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 0.048 (234 hom., cov: 31)
• Consequence: LINC00881 ENST00000460796.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 13 publications found

Genes affected

LINC00881 (HGNC:48567): (long intergenic non-protein coding RNA 881)

LOC101928236 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928236	XR_007096141.1	n.1498-6800C>T		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00881	ENST00000460796.2	n.168-6800C>T		intron_variant	Intron 1 of 1	3
LINC00881	ENST00000475102.1	n.19+2493C>T		intron_variant	Intron 1 of 3	5
LINC00881	ENST00000487238.5	n.122-6800C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7322 AN: 152006 Hom.: 230 Cov.: 31

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0761

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0421

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0483 AC: 7341 AN: 152124 Hom.: 234 Cov.: 31 AF XY: 0.0508 AC XY: 3780 AN XY: 74362

African (AFR) AF: 0.0344 AC: 1426 AN: 41494

American (AMR) AF: 0.0766 AC: 1171 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.0823 AC: 425 AN: 5166

South Asian (SAS) AF: 0.0854 AC: 412 AN: 4822

European-Finnish (FIN) AF: 0.0796 AC: 842 AN: 10572

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0420 AC: 2858 AN: 68000

Other (OTH) AF: 0.0322 AC: 68 AN: 2114

Alfa AF: 0.0452 Hom.: 549

Bravo AF: 0.0483

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.80
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs9866141; hg19: chr3-156950579;