chr3-157167548-C-T

Variant names:

• chr3-157167548-C-T
• rs7647643
• ENST00000480817.1:n.204-1469C>T

Variant summary

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

The ENST00000480817.1(LINC00881):​n.204-1469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,950 control chromosomes in the GnomAD database, including 12,630 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 0.40 (12630 hom., cov: 32)
• Consequence: LINC00881 ENST00000480817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 7 publications found

Genes affected

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

ENSG00000301840 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000480817.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00881	ENST00000480817.1	TSL:3	n.204-1469C>T		intron	N/A
	LINC00881	ENST00000781925.1		n.342-1469C>T		intron	N/A
	LINC00881	ENST00000781926.1		n.510-1469C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60683 AN: 151832 Hom.: 12611 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.400 AC: 60749 AN: 151950 Hom.: 12630 Cov.: 32 AF XY: 0.404 AC XY: 29975 AN XY: 74250

African (AFR) AF: 0.440 AC: 18232 AN: 41412

American (AMR) AF: 0.559 AC: 8543 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1128 AN: 3464

East Asian (EAS) AF: 0.577 AC: 2974 AN: 5158

South Asian (SAS) AF: 0.404 AC: 1945 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3157 AN: 10548

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23396 AN: 67952

Other (OTH) AF: 0.390 AC: 825 AN: 2114

Alfa AF: 0.369 Hom.: 1720

Bravo AF: 0.425

Asia WGS AF: 0.505 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.8
DANN	Benign	0.75
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7647643; hg19: chr3-156885337;