rs7641989

Positions:

• chr3-138940493-G-A
• chr3-138940493-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121649.1(LINC01391):​n.290+1891C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,732 control chromosomes in the GnomAD database, including 6,806 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 0.22 (6806 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01391 NR_121649.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01391	NR_121649.1	n.290+1891C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01391	ENST00000495287.1	n.290+1891C>T		intron_variant, non_coding_transcript_variant		2
LINC01391	ENST00000477059.1	n.418C>T		non_coding_transcript_exon_variant	2/2	3
LINC01391	ENST00000483650.1	n.336+1828C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33676 AN: 151614 Hom.: 6779 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.190

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.223 AC: 33765 AN: 151732 Hom.: 6806 Cov.: 32 AF XY: 0.228 AC XY: 16915 AN XY: 74090

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.0520

Gnomad4 OTH AF: 0.196

Alfa AF: 0.0975 Hom.: 441

Bravo AF: 0.246

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7641989; hg19: chr3-138659335;