rs4686914

Variant names:

• chr3-187999752-C-T
• rs4686914
• ENST00000415940.1:n.91-1994G>A

Variant summary

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

The ENST00000744770.1(LINC01991):​n.316-1994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,058 control chromosomes in the GnomAD database, including 6,047 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 0.27 (6047 hom., cov: 32)
• Consequence: LINC01991 ENST00000744770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 22 publications found

Genes affected

LINC01991 (HGNC:52823): (long intergenic non-protein coding RNA 1991)

LOC107986166 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744770.1. 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
	LINC01991	ENST00000415940.1	TSL:5	n.91-1994G>A		intron	N/A
	LINC01991	ENST00000744770.1		n.316-1994G>A		intron	N/A
	LINC01991	ENST00000744771.1		n.304-1994G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41183 AN: 151940 Hom.: 6042 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.271 AC: 41206 AN: 152058 Hom.: 6047 Cov.: 32 AF XY: 0.273 AC XY: 20273 AN XY: 74324

African (AFR) AF: 0.161 AC: 6678 AN: 41482

American (AMR) AF: 0.283 AC: 4320 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2078 AN: 5182

South Asian (SAS) AF: 0.215 AC: 1040 AN: 4826

European-Finnish (FIN) AF: 0.336 AC: 3538 AN: 10544

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21520 AN: 67956

Other (OTH) AF: 0.303 AC: 640 AN: 2114

Alfa AF: 0.300 Hom.: 19990

Bravo AF: 0.264

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4686914; hg19: chr3-187717540;