rs11596008

Positions:

• chr10-99527557-C-T

Variant summary

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

The NR_120618.1(LINC01475):​n.577+249G>A 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 0.286 in 152,218 control chromosomes in the GnomAD database, including 7,159 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 0.29 (7156 hom., cov: 33)
  • Exomes 𝑓: 0.19 (3 hom.)
• Consequence: LINC01475 NR_120618.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

Genes affected

(HGNC:):

LINC01475 (HGNC:51113): (long intergenic non-protein coding RNA 1475)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01475	NR_120618.1	n.577+249G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000452494.2	n.257+353C>T		intron_variant, non_coding_transcript_variant		1
LINC01475	ENST00000548010.1	n.577+249G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43386 AN: 151988 Hom.: 7141 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.188 AC: 21 AN: 112 Hom.: 3 AF XY: 0.209 AC XY: 18 AN XY: 86

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.286 AC: 43445 AN: 152106 Hom.: 7156 Cov.: 33 AF XY: 0.281 AC XY: 20895 AN XY: 74390

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.260

Alfa AF: 0.268 Hom.: 1295

Bravo AF: 0.299

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11596008; hg19: chr10-101287314;