14-45707898-A-C

Variant names:

• chr14-45707898-A-C
• rs1906810
• ENST00000557602.1:n.171T>G

Variant summary

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

The ENST00000761743.1(LINC02303):​n.76T>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 ENST00000761743.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 2 publications found

Genes affected

LINC02303 (HGNC:53222): (long intergenic non-protein coding RNA 2303)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761743.1. 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
	LINC02303	NR_146546.1		n.309-1396T>G		intron	N/A
	LINC02303	NR_146547.1		n.254-1396T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02303	ENST00000557602.1	TSL:5	n.171T>G		splice_region non_coding_transcript_exon	Exon 2 of 3
	LINC02303	ENST00000761743.1		n.76T>G		splice_region non_coding_transcript_exon	Exon 2 of 3
	LINC02303	ENST00000554431.5	TSL:2	n.193-1396T>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.206 AC: 8559 AN: 41524

American (AMR) AF: 0.304 AC: 4647 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1453 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3198 AN: 5156

South Asian (SAS) AF: 0.473 AC: 2275 AN: 4814

European-Finnish (FIN) AF: 0.425 AC: 4490 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28793 AN: 67938

Other (OTH) AF: 0.334 AC: 703 AN: 2106

Alfa AF: 0.393 Hom.: 2519

Bravo AF: 0.342

Asia WGS AF: 0.523 AC: 1812 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.68
PhyloP100		0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1906810;

hg19: chr14-46177101;