ENST00000418245.5:n.423C>T

Variant names:

• chr1-204037469-G-A
• rs4951039
• ENST00000418245.5:n.423C>T

Variant summary

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

The ENST00000418245.5(LINC00303):​n.423C>T 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 0.872 in 519,518 control chromosomes in the GnomAD database, including 198,142 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 0.88 (59777 hom., cov: 32)
  • Exomes 𝑓: 0.87 (138365 hom.)
• Consequence: LINC00303 ENST00000418245.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 14 publications found

Genes affected

LINC00303 (HGNC:26865): (long intergenic non-protein coding RNA 303)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00303	NR_027902.2	n.424C>T		non_coding_transcript_exon_variant	Exon 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00303	ENST00000418245.5	n.423C>T		non_coding_transcript_exon_variant	Exon 3 of 5	1
LINC00303	ENST00000427799.1	n.424C>T		non_coding_transcript_exon_variant	Exon 3 of 6	1
LINC00303	ENST00000367207.7	n.424C>T		non_coding_transcript_exon_variant	Exon 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134566 AN: 152098 Hom.: 59736 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.907

GnomAD2 exomes AF: 0.871 AC: 206193 AN: 236654 AF XY: 0.867

Gnomad AFR exome AF: 0.933

Gnomad AMR exome AF: 0.945

Gnomad ASJ exome AF: 0.928

Gnomad EAS exome AF: 0.737

Gnomad FIN exome AF: 0.845

Gnomad NFE exome AF: 0.871

Gnomad OTH exome AF: 0.881

GnomAD4 exome AF: 0.866 AC: 318259 AN: 367302 Hom.: 138365 Cov.: 0 AF XY: 0.862 AC XY: 181472 AN XY: 210554

African (AFR) AF: 0.927 AC: 9722 AN: 10488

American (AMR) AF: 0.945 AC: 34293 AN: 36270

Ashkenazi Jewish (ASJ) AF: 0.928 AC: 10882 AN: 11728

East Asian (EAS) AF: 0.749 AC: 9864 AN: 13162

South Asian (SAS) AF: 0.827 AC: 55159 AN: 66726

European-Finnish (FIN) AF: 0.850 AC: 15326 AN: 18026

Middle Eastern (MID) AF: 0.926 AC: 2404 AN: 2596

European-Non Finnish (NFE) AF: 0.867 AC: 166200 AN: 191730

Other (OTH) AF: 0.869 AC: 14409 AN: 16576

GnomAD4 genome AF: 0.885 AC: 134663 AN: 152216 Hom.: 59777 Cov.: 32 AF XY: 0.881 AC XY: 65567 AN XY: 74402

African (AFR) AF: 0.931 AC: 38696 AN: 41548

American (AMR) AF: 0.920 AC: 14056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3217 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3902 AN: 5168

South Asian (SAS) AF: 0.812 AC: 3914 AN: 4818

European-Finnish (FIN) AF: 0.836 AC: 8850 AN: 10580

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 59003 AN: 68022

Other (OTH) AF: 0.907 AC: 1920 AN: 2116

Alfa AF: 0.878 Hom.: 182926

Bravo AF: 0.895

Asia WGS AF: 0.780 AC: 2713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.078
DANN	Benign	0.65
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4951039; hg19: chr1-204006597;