rs7641989

Variant names:

• chr3-138940493-G-A
• rs7641989
• ENST00000477059.2:n.507C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000477059.2(LINC01391):​n.507C>T variant causes a non coding transcript exon 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 ENST00000477059.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000477059.2. 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.290+1891C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01391	ENST00000477059.2	TSL:3	n.507C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01391	ENST00000774123.1		n.567C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01391	ENST00000483650.1	TSL:3	n.336+1828C>T		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.481 AC: 19876 AN: 41338

American (AMR) AF: 0.262 AC: 3993 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3330 AN: 5154

South Asian (SAS) AF: 0.169 AC: 809 AN: 4798

European-Finnish (FIN) AF: 0.149 AC: 1556 AN: 10468

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0520 AC: 3535 AN: 67960

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.107 Hom.: 530

Bravo AF: 0.246

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.79
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7641989; hg19: chr3-138659335;