rs134378

Variant names:

• chr22-35173697-T-G
• rs134378
• ENST00000423311.1:n.223-1237A>C

Variant summary

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

The ENST00000423311.1(LINC01399):​n.223-1237A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 152,162 control chromosomes in the GnomAD database, including 27,382 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 0.55 (27382 hom., cov: 34)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.223-1237A>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000423311.1	n.223-1237A>C		intron_variant	Intron 2 of 5	3
LINC01399	ENST00000798716.1	n.63-1237A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84142 AN: 152046 Hom.: 27384 Cov.: 34

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.553 AC: 84143 AN: 152162 Hom.: 27382 Cov.: 34 AF XY: 0.555 AC XY: 41291 AN XY: 74394

African (AFR) AF: 0.196 AC: 8120 AN: 41530

American (AMR) AF: 0.656 AC: 10032 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2492 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2106 AN: 5174

South Asian (SAS) AF: 0.589 AC: 2844 AN: 4826

European-Finnish (FIN) AF: 0.706 AC: 7466 AN: 10580

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48989 AN: 67972

Other (OTH) AF: 0.595 AC: 1257 AN: 2114

Alfa AF: 0.677 Hom.: 60803

Bravo AF: 0.537

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.37
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs134378; hg19: chr22-35569690;