rs5999715

Variant names:

• chr22-35097374-C-A
• rs5999715
• ENST00000798716.1:n.353-21117G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-35097374-C-A
• chr22-35097374-C-T

Variant summary

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

The ENST00000798716.1(LINC01399):​n.353-21117G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,252 control chromosomes in the GnomAD database, including 2,403 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 0.10 (2403 hom., cov: 33)
• Consequence: LINC01399 ENST00000798716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 2 publications found

Genes affected

LINC01399 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798716.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01399	ENST00000798716.1		n.353-21117G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15262 AN: 152136 Hom.: 2391 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.101 AC: 15319 AN: 152252 Hom.: 2403 Cov.: 33 AF XY: 0.0974 AC XY: 7252 AN XY: 74444

African (AFR) AF: 0.337 AC: 13977 AN: 41498

American (AMR) AF: 0.0355 AC: 544 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5184

South Asian (SAS) AF: 0.0353 AC: 170 AN: 4822

European-Finnish (FIN) AF: 0.00960 AC: 102 AN: 10624

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.00237 AC: 161 AN: 68030

Other (OTH) AF: 0.0691 AC: 146 AN: 2114

Alfa AF: 0.0322 Hom.: 762

Bravo AF: 0.112

Asia WGS AF: 0.0810 AC: 284 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.42
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs5999715; hg19: chr22-35493367;