1-204037410-T-C

Position:

• chr1-204037410-T-C

Variant summary

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

The ENST00000367207.7(LINC00303):​n.483A>G 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 0.883 in 515,832 control chromosomes in the GnomAD database, including 202,030 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 0.90 (62149 hom., cov: 31)
  • Exomes 𝑓: 0.88 (139881 hom.)
• Consequence: LINC00303 ENST00000367207.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00303	NR_027902.2	n.432+51A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00303	ENST00000367207.7	n.483A>G		non_coding_transcript_exon_variant	3/5	2
LINC00303	ENST00000418245.5	n.482A>G		non_coding_transcript_exon_variant	3/5	1
LINC00303	ENST00000427799.1	n.432+51A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137077 AN: 152042 Hom.: 62096 Cov.: 31

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.925

GnomAD4 exome AF: 0.876 AC: 318453 AN: 363672 Hom.: 139881 Cov.: 0 AF XY: 0.872 AC XY: 182038 AN XY: 208786

Gnomad4 AFR exome AF: 0.977

Gnomad4 AMR exome AF: 0.952

Gnomad4 ASJ exome AF: 0.938

Gnomad4 EAS exome AF: 0.787

Gnomad4 SAS exome AF: 0.847

Gnomad4 FIN exome AF: 0.850

Gnomad4 NFE exome AF: 0.870

Gnomad4 OTH exome AF: 0.880

GnomAD4 genome AF: 0.902 AC: 137187 AN: 152160 Hom.: 62149 Cov.: 31 AF XY: 0.898 AC XY: 66813 AN XY: 74370

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.925

Alfa AF: 0.872 Hom.: 22431

Bravo AF: 0.913

Asia WGS AF: 0.819 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4951291; hg19: chr1-204006538;