rs12651676

Variant names:

• chr4-4844346-A-G
• rs12651676
• ENST00000652410.1:n.128A>G

Variant summary

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

The ENST00000652410.1(LINC01396):​n.128A>G 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 0.515 in 152,136 control chromosomes in the GnomAD database, including 20,355 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 0.51 (20352 hom., cov: 34)
  • Exomes 𝑓: 0.50 (3 hom.)
• Consequence: LINC01396 ENST00000652410.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 1 publications found

Genes affected

LINC01396 (HGNC:50675): (long intergenic non-protein coding RNA 1396)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01396	NR_125765.1	n.-91A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01396	ENST00000652410.1	n.128A>G		non_coding_transcript_exon_variant	Exon 1 of 4
LINC01396	ENST00000662851.1	n.159A>G		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01396	ENST00000724736.1	n.159A>G		non_coding_transcript_exon_variant	Exon 1 of 2
LINC01396	ENST00000609099.1	n.-91A>G		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78273 AN: 152006 Hom.: 20344 Cov.: 34

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.515

GnomAD4 exome AF: 0.500 AC: 6 AN: 12 Hom.: 3 AF XY: 0.600 AC XY: 6 AN XY: 10

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) AF: 0.500 AC: 6 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.515 AC: 78313 AN: 152124 Hom.: 20352 Cov.: 34 AF XY: 0.515 AC XY: 38320 AN XY: 74352

African (AFR) AF: 0.487 AC: 20180 AN: 41476

American (AMR) AF: 0.468 AC: 7164 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1500 AN: 3472

East Asian (EAS) AF: 0.720 AC: 3722 AN: 5172

South Asian (SAS) AF: 0.548 AC: 2644 AN: 4828

European-Finnish (FIN) AF: 0.532 AC: 5626 AN: 10576

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35771 AN: 67986

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

Alfa AF: 0.524 Hom.: 2611

Bravo AF: 0.508

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.25
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12651676; hg19: chr4-4846073;