rs12524120

Variant names:

• chr6-1365415-T-A
• rs12524120
• ENST00000721686.1:n.89+25577A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-1365415-T-A
• chr6-1365415-T-C

Variant summary

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

The ENST00000721686.1(LINC01394):​n.89+25577A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0749 in 152,308 control chromosomes in the GnomAD database, including 616 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 0.075 (616 hom., cov: 33)
• Consequence: LINC01394 ENST00000721686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 1 publications found

Genes affected

LINC01394 (HGNC:50670): (long intergenic non-protein coding RNA 1394)

FOXF2-DT (HGNC:50662): (FOXF2 divergent transcript)

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 (AMR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2-DT	NR_187218.1	n.443+23604A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01394	ENST00000721686.1	n.89+25577A>T		intron_variant	Intron 1 of 2
LINC01394	ENST00000721687.1	n.276+23604A>T		intron_variant	Intron 2 of 3
LINC01394	ENST00000721688.1	n.346+23604A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0750 AC: 11407 AN: 152190 Hom.: 616 Cov.: 33

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0769

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

GnomAD4 genome AF: 0.0749 AC: 11412 AN: 152308 Hom.: 616 Cov.: 33 AF XY: 0.0755 AC XY: 5624 AN XY: 74474

African (AFR) AF: 0.0183 AC: 762 AN: 41594

American (AMR) AF: 0.103 AC: 1581 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5192

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4826

European-Finnish (FIN) AF: 0.144 AC: 1527 AN: 10588

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7007 AN: 68016

Other (OTH) AF: 0.0756 AC: 160 AN: 2116

Alfa AF: 0.0448 Hom.: 49

Bravo AF: 0.0718

Asia WGS AF: 0.0150 AC: 52 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	0.11
DANN	Benign	0.49
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12524120; hg19: chr6-1365650;