rs6695249

chr1-84631237-A-Gchr1-84631237-A-T

Variant summary

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

The NR_027379.1(LINC01555):n.227-350T>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 0.182 in 367,004 control chromosomes in the GnomAD database, including 6,801 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 0.19 (2851 hom., cov: 32)
  • Exomes 𝑓: 0.18 (3950 hom.)
• Consequence: LINC01555 NR_027379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

LINC01555 (HGNC:26647): (long intergenic non-protein coding RNA 1555)

LOC124904206 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01555	NR_027379.1	n.227-350T>C		intron_variant, non_coding_transcript_variant
LOC124904206	XR_007066196.1	n.298-94A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01555	ENST00000370624.1	n.227-350T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28411 AN: 152076 Hom.: 2834 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.178 AC: 38251 AN: 214806 Hom.: 3950 AF XY: 0.185 AC XY: 22188 AN XY: 120238

Gnomad4 AFR exome AF: 0.246

Gnomad4 AMR exome AF: 0.257

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.0559

Gnomad4 SAS exome AF: 0.237

Gnomad4 FIN exome AF: 0.129

Gnomad4 NFE exome AF: 0.154

Gnomad4 OTH exome AF: 0.174

GnomAD4 genome AF: 0.187 AC: 28475 AN: 152198 Hom.: 2851 Cov.: 32 AF XY: 0.187 AC XY: 13887 AN XY: 74426

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0594

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.195

Alfa AF: 0.171 Hom.: 3054

Bravo AF: 0.196

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6695249; hg19: chr1-85096920; COSMIC: COSV59226043;