rs134220

Variant names:

• chr22-35134490-T-C
• rs134220
• ENST00000423311.1:n.513-14423A>G

Variant summary

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

The ENST00000423311.1(LINC01399):​n.513-14423A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,224 control chromosomes in the GnomAD database, including 1,145 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 0.12 (1145 hom., cov: 32)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.810
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.513-14423A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000423311.1	n.513-14423A>G		intron_variant	Intron 4 of 5	3
LINC01399	ENST00000798716.1	n.352+36945A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17900 AN: 152106 Hom.: 1146 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.118 AC: 17905 AN: 152224 Hom.: 1145 Cov.: 32 AF XY: 0.118 AC XY: 8762 AN XY: 74420

African (AFR) AF: 0.101 AC: 4191 AN: 41526

American (AMR) AF: 0.0954 AC: 1460 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3470

East Asian (EAS) AF: 0.00753 AC: 39 AN: 5182

South Asian (SAS) AF: 0.112 AC: 537 AN: 4812

European-Finnish (FIN) AF: 0.153 AC: 1622 AN: 10600

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9324 AN: 68006

Other (OTH) AF: 0.107 AC: 227 AN: 2114

Alfa AF: 0.126 Hom.: 2321

Bravo AF: 0.109

Asia WGS AF: 0.0680 AC: 235 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	2.0
DANN	Benign	0.44
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs134220; hg19: chr22-35530483;