rs750321

Variant names:

• chr3-138939353-T-C
• rs750321
• ENST00000483650.1:n.337-917A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-138939353-T-C
• chr3-138939353-T-G

Variant summary

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

The ENST00000495287.1(LINC01391):​n.291-917A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,300 control chromosomes in the GnomAD database, including 1,123 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 0.062 (1123 hom., cov: 33)
• Consequence: LINC01391 ENST00000495287.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 0 publications found

Genes affected

LINC01391 (HGNC:50666): (long intergenic non-protein coding RNA 1391)

ENSG00000300820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000495287.1. 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
	LINC01391	NR_121649.1		n.291-917A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01391	ENST00000483650.1	TSL:3	n.337-917A>G		intron	N/A
	LINC01391	ENST00000495287.1	TSL:2	n.291-917A>G		intron	N/A
	ENSG00000300820	ENST00000774246.1		n.*9T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9405 AN: 152182 Hom.: 1125 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00608

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0619 AC: 9420 AN: 152300 Hom.: 1123 Cov.: 33 AF XY: 0.0646 AC XY: 4810 AN XY: 74464

African (AFR) AF: 0.117 AC: 4865 AN: 41554

American (AMR) AF: 0.0304 AC: 465 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.549 AC: 2836 AN: 5166

South Asian (SAS) AF: 0.0553 AC: 267 AN: 4828

European-Finnish (FIN) AF: 0.0275 AC: 292 AN: 10614

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00609 AC: 414 AN: 68036

Other (OTH) AF: 0.0629 AC: 133 AN: 2114

Alfa AF: 0.0300 Hom.: 2195

Bravo AF: 0.0665

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.68
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs750321; hg19: chr3-138658195;