rs11596008

Variant names:

• chr10-99527557-C-T
• rs11596008
• ENST00000452494.3:n.1522+353C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000795235.1(LINC01475):​n.98G>A variant causes a non coding transcript exon 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 ENST00000795235.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 5 publications found

Genes affected

ENSG00000228778 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01475	NR_120618.1		n.577+249G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228778	ENST00000452494.3	TSL:1	n.1522+353C>T		intron	N/A
	LINC01475	ENST00000548010.2	TSL:1	n.654+249G>A		intron	N/A
	LINC01475	ENST00000795235.1		n.98G>A		non_coding_transcript_exon	Exon 1 of 4

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.0833 AC: 1 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.189 AC: 17 AN: 90

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.430 AC: 17843 AN: 41482

American (AMR) AF: 0.262 AC: 4003 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3468

East Asian (EAS) AF: 0.115 AC: 593 AN: 5146

South Asian (SAS) AF: 0.415 AC: 2002 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1420 AN: 10618

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15879 AN: 67962

Other (OTH) AF: 0.260 AC: 546 AN: 2102

Alfa AF: 0.272 Hom.: 1513

Bravo AF: 0.299

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.1
DANN	Benign	0.82
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11596008; hg19: chr10-101287314;