22-35121680-T-C

Variant names:

• chr22-35121680-T-C
• rs7284619
• ENST00000423311.1:n.513-1613A>G

Variant summary

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

The ENST00000423311.1(LINC01399):​n.513-1613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,088 control chromosomes in the GnomAD database, including 5,287 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 0.23 (5287 hom., cov: 32)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01399	NR_126356.1	n.513-1613A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01399	ENST00000423311.1	n.513-1613A>G		intron_variant	Intron 4 of 5	3
LINC01399	ENST00000798716.1	n.353-45423A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35456 AN: 151970 Hom.: 5271 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.234 AC: 35514 AN: 152088 Hom.: 5287 Cov.: 32 AF XY: 0.228 AC XY: 16941 AN XY: 74350

African (AFR) AF: 0.421 AC: 17456 AN: 41416

American (AMR) AF: 0.134 AC: 2048 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3472

East Asian (EAS) AF: 0.0737 AC: 382 AN: 5182

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4812

European-Finnish (FIN) AF: 0.140 AC: 1480 AN: 10602

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11723 AN: 67994

Other (OTH) AF: 0.204 AC: 431 AN: 2116

Alfa AF: 0.193 Hom.: 1153

Bravo AF: 0.237

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.77
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7284619; hg19: chr22-35517673;