8-11578007-T-C

Position:

• chr8-11578007-T-C

Variant summary

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

The NR_040035.1(LINC00208):​n.784-363T>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 0.506 in 151,892 control chromosomes in the GnomAD database, including 20,677 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 0.51 (20677 hom., cov: 31)
• Consequence: LINC00208 NR_040035.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77

Genes affected

LINC00208 (HGNC:15535): (long intergenic non-protein coding RNA 208)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00208	NR_040035.1	n.784-363T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00208	ENST00000661938.1	n.1029-363T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76774 AN: 151774 Hom.: 20671 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.0199

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.506 AC: 76819 AN: 151892 Hom.: 20677 Cov.: 31 AF XY: 0.490 AC XY: 36409 AN XY: 74232

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.510

Alfa AF: 0.547 Hom.: 4835

Bravo AF: 0.506

Asia WGS AF: 0.210 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10108511; hg19: chr8-11435516;