rs750321

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01391 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01391	NR_121649.1	n.291-917A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01391	ENST00000483650.1	n.337-917A>G		intron_variant		3
LINC01391	ENST00000495287.1	n.291-917A>G		intron_variant		2

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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0304

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.0553

Gnomad4 FIN AF: 0.0275

Gnomad4 NFE AF: 0.00609

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0223 Hom.: 705

Bravo AF: 0.0665

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750321; hg19: chr3-138658195;