chr1-204037469-G-A

Position:

• chr1-204037469-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00303 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00303	NR_027902.2	n.424C>T		non_coding_transcript_exon_variant	3/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00303	ENST00000418245.5	n.423C>T		non_coding_transcript_exon_variant	3/5	1
LINC00303	ENST00000427799.1	n.424C>T		non_coding_transcript_exon_variant	3/6	1
LINC00303	ENST00000367207.7	n.424C>T		non_coding_transcript_exon_variant	3/5	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

GnomAD3 exomes AF: 0.871 AC: 206193 AN: 236654 Hom.: 90259 AF XY: 0.867 AC XY: 111946 AN XY: 129146

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 SAS exome AF: 0.827

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

Gnomad4 AFR exome AF: 0.927

Gnomad4 AMR exome AF: 0.945

Gnomad4 ASJ exome AF: 0.928

Gnomad4 EAS exome AF: 0.749

Gnomad4 SAS exome AF: 0.827

Gnomad4 FIN exome AF: 0.850

Gnomad4 NFE exome AF: 0.867

Gnomad4 OTH exome AF: 0.869

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

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.907

Alfa AF: 0.879 Hom.: 84002

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4951039; hg19: chr1-204006597;