rs7284619

chr22-35121680-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_126356.1(LINC01399):n.513-1613A>G variant causes a intron, non coding transcript 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 NR_126356.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01399	NR_126356.1	n.513-1613A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01399	ENST00000423311.1	n.513-1613A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0737

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.204

Alfa AF: 0.190 Hom.: 964

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7284619; hg19: chr22-35517673;