rs713969

Variant names:

• chr22-35203000-C-A
• rs713969
• ENST00000423311.1:n.60-7981G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-35203000-C-A
• chr22-35203000-C-G

Variant summary

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

The ENST00000423311.1(LINC01399):​n.60-7981G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 152,006 control chromosomes in the GnomAD database, including 18,913 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 0.44 (18913 hom., cov: 32)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 5 publications found

Genes affected

LINC01399 (HGNC:):

LINC01399 (HGNC:50680): (long intergenic non-protein coding RNA 1399)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.60-7981G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000423311.1	n.60-7981G>T		intron_variant	Intron 1 of 5	3
LINC01399	ENST00000798716.1	n.62+27998G>T		intron_variant	Intron 1 of 3
LINC01399	ENST00000798717.1	n.59-7981G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67390 AN: 151888 Hom.: 18864 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.444 AC: 67497 AN: 152006 Hom.: 18913 Cov.: 32 AF XY: 0.442 AC XY: 32825 AN XY: 74270

African (AFR) AF: 0.793 AC: 32886 AN: 41468

American (AMR) AF: 0.342 AC: 5232 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3106 AN: 5150

South Asian (SAS) AF: 0.410 AC: 1964 AN: 4794

European-Finnish (FIN) AF: 0.294 AC: 3114 AN: 10588

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 18999 AN: 67952

Other (OTH) AF: 0.403 AC: 849 AN: 2108

Alfa AF: 0.322 Hom.: 5922

Bravo AF: 0.460

Asia WGS AF: 0.508 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.55
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs713969; hg19: chr22-35598993;