chr3-187999098-A-G

Variant names:

• chr3-187999098-A-G
• rs1553091
• ENST00000415940.1:n.91-1340T>C

Variant summary

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

The ENST00000415940.1(LINC01991):​n.91-1340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,064 control chromosomes in the GnomAD database, including 6,520 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 0.28 (6520 hom., cov: 32)
• Consequence: LINC01991 ENST00000415940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 10 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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986166	XR_001741061.2	n.416-1340T>C		intron_variant	Intron 4 of 4
LOC107986166	XR_001741062.2	n.317-1340T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01991	ENST00000415940.1	n.91-1340T>C		intron_variant	Intron 1 of 1	5
LINC01991	ENST00000744770.1	n.316-1340T>C		intron_variant	Intron 2 of 3
LINC01991	ENST00000744771.1	n.304-1340T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42655 AN: 151944 Hom.: 6518 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.281 AC: 42676 AN: 152064 Hom.: 6520 Cov.: 32 AF XY: 0.284 AC XY: 21138 AN XY: 74336

African (AFR) AF: 0.163 AC: 6770 AN: 41494

American (AMR) AF: 0.301 AC: 4601 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3468

East Asian (EAS) AF: 0.436 AC: 2254 AN: 5172

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3936 AN: 10554

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

European-Non Finnish (NFE) AF: 0.324 AC: 21987 AN: 67952

Other (OTH) AF: 0.308 AC: 650 AN: 2110

Alfa AF: 0.306 Hom.: 18656

Bravo AF: 0.273

Asia WGS AF: 0.316 AC: 1097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs1553091; hg19: chr3-187716886;