1-204037410-T-C

Variant names:

• chr1-204037410-T-C
• rs4951291
• ENST00000418245.5:n.482A>G

Variant summary

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

The ENST00000418245.5(LINC00303):​n.482A>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 ENST00000418245.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418245.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00303	NR_027902.2		n.432+51A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00303	ENST00000418245.5	TSL:1	n.482A>G		non_coding_transcript_exon	Exon 3 of 5
	LINC00303	ENST00000427799.1	TSL:1	n.432+51A>G		intron	N/A
	LINC00303	ENST00000367207.7	TSL:2	n.483A>G		non_coding_transcript_exon	Exon 3 of 5

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

African (AFR) AF: 0.977 AC: 10047 AN: 10286

American (AMR) AF: 0.952 AC: 33783 AN: 35478

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 10909 AN: 11626

East Asian (EAS) AF: 0.787 AC: 10332 AN: 13134

South Asian (SAS) AF: 0.847 AC: 56076 AN: 66184

European-Finnish (FIN) AF: 0.850 AC: 15319 AN: 18016

Middle Eastern (MID) AF: 0.938 AC: 1357 AN: 1446

European-Non Finnish (NFE) AF: 0.870 AC: 166234 AN: 191140

Other (OTH) AF: 0.880 AC: 14396 AN: 16362

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

African (AFR) AF: 0.976 AC: 40533 AN: 41526

American (AMR) AF: 0.932 AC: 14247 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3246 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4112 AN: 5172

South Asian (SAS) AF: 0.832 AC: 4003 AN: 4814

European-Finnish (FIN) AF: 0.837 AC: 8838 AN: 10564

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59136 AN: 68010

Other (OTH) AF: 0.925 AC: 1958 AN: 2116

Alfa AF: 0.873 Hom.: 25442

Bravo AF: 0.913

Asia WGS AF: 0.819 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.35
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4951291; hg19: chr1-204006538;