rs10504368

chr8-63871986-A-G

Variant summary

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

The NR_125826.1(LINC01414):n.411-14875T>C 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 0.278 in 152,142 control chromosomes in the GnomAD database, including 6,257 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 0.28 (6257 hom., cov: 32)
• Consequence: LINC01414 NR_125826.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208

Genes affected

LINC01414 (HGNC:50707): (long intergenic non-protein coding RNA 1414)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01414	NR_125826.1	n.411-14875T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01414	ENST00000523191.5	n.422-22991T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42210 AN: 152024 Hom.: 6253 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.278 AC: 42227 AN: 152142 Hom.: 6257 Cov.: 32 AF XY: 0.282 AC XY: 20984 AN XY: 74364

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.273

Alfa AF: 0.285 Hom.: 779

Bravo AF: 0.278

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.21
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504368; hg19: chr8-64784543;