rs4968382

Positions:

• chr17-59515354-G-A

Variant summary

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

The NR_110813.1(LINC01476):​n.378+11126C>T 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 0.433 in 151,866 control chromosomes in the GnomAD database, including 18,555 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 0.43 (18555 hom., cov: 31)
• Consequence: LINC01476 NR_110813.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

LINC01476 (HGNC:51117): (long intergenic non-protein coding RNA 1476)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01476	NR_110813.1	n.378+11126C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01476	ENST00000665301.2	n.372+11126C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65610 AN: 151748 Hom.: 18488 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.433 AC: 65720 AN: 151866 Hom.: 18555 Cov.: 31 AF XY: 0.435 AC XY: 32269 AN XY: 74182

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.407

Alfa AF: 0.345 Hom.: 2001

Bravo AF: 0.451

Asia WGS AF: 0.548 AC: 1907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4968382; hg19: chr17-57592715;