rs1906810

Positions:

• chr14-45707898-A-C
• chr14-45707898-A-T

Variant summary

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

The ENST00000557602.1(LINC02303):​n.171T>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,066 control chromosomes in the GnomAD database, including 10,777 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 0.36 (10777 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC02303 ENST00000557602.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

Genes affected

LINC02303 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02303	NR_146546.1	n.309-1396T>G		intron_variant
LINC02303	NR_146547.1	n.254-1396T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02303	ENST00000557602.1	n.171T>G		splice_region_variant, non_coding_transcript_exon_variant	2/3	5
LINC02303	ENST00000554431.5	n.193-1396T>G		intron_variant		2
LINC02303	ENST00000554711.5	n.287-1396T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54577 AN: 151946 Hom.: 10773 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.332

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.359 AC: 54585 AN: 152066 Hom.: 10777 Cov.: 33 AF XY: 0.360 AC XY: 26777 AN XY: 74358

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.334

Alfa AF: 0.397 Hom.: 2499

Bravo AF: 0.342

Asia WGS AF: 0.523 AC: 1812 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1906810; hg19: chr14-46177101;