rs7750826

Variant names:

• chr6-1336632-A-G
• rs7750826
• ENST00000721686.1:n.90-11705T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-1336632-A-G
• chr6-1336632-A-T

Variant summary

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

The ENST00000721686.1(LINC01394):​n.90-11705T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,162 control chromosomes in the GnomAD database, including 4,956 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 0.25 (4956 hom., cov: 33)
• Consequence: LINC01394 ENST00000721686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 6 publications found

Genes affected

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

ENSG00000294194 (HGNC:):

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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXF2-DT	NR_187218.1	n.444-11705T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01394	ENST00000721686.1	n.90-11705T>C		intron_variant	Intron 1 of 2
LINC01394	ENST00000721687.1	n.277-11705T>C		intron_variant	Intron 2 of 3
LINC01394	ENST00000721688.1	n.347-11705T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37346 AN: 152044 Hom.: 4951 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.246 AC: 37370 AN: 152162 Hom.: 4956 Cov.: 33 AF XY: 0.254 AC XY: 18885 AN XY: 74370

African (AFR) AF: 0.187 AC: 7753 AN: 41514

American (AMR) AF: 0.334 AC: 5108 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1820 AN: 5176

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3300 AN: 10570

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16774 AN: 68008

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.245 Hom.: 14046

Bravo AF: 0.244

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.0
DANN	Benign	0.88
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs7750826; hg19: chr6-1336867;