3-196180782-T-C

Variant names:

• chr3-196180782-T-C
• rs4916483
• ENST00000744814.1:n.1166+2630T>C

Variant summary

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

The ENST00000744814.1(LINC00885):​n.1166+2630T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,168 control chromosomes in the GnomAD database, including 1,934 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 0.13 (1934 hom., cov: 31)
• Consequence: LINC00885 ENST00000744814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 28 publications found

Genes affected

LINC00885 (HGNC:48571): (long intergenic non-protein coding RNA 885)

ENSG00000297061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744814.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00885	ENST00000744814.1		n.1166+2630T>C		intron	N/A
	ENSG00000297061	ENST00000745039.1		n.328+3694A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19122 AN: 152052 Hom.: 1921 Cov.: 31

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.126 AC: 19144 AN: 152168 Hom.: 1934 Cov.: 31 AF XY: 0.132 AC XY: 9784 AN XY: 74380

African (AFR) AF: 0.0298 AC: 1238 AN: 41548

American (AMR) AF: 0.224 AC: 3419 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 490 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2541 AN: 5160

South Asian (SAS) AF: 0.286 AC: 1380 AN: 4818

European-Finnish (FIN) AF: 0.0822 AC: 870 AN: 10590

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8683 AN: 68004

Other (OTH) AF: 0.163 AC: 344 AN: 2114

Alfa AF: 0.136 Hom.: 7781

Bravo AF: 0.130

Asia WGS AF: 0.395 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4916483; hg19: chr3-195907653;