2-228566205-T-C

Position:

• chr2-228566205-T-C

Variant summary

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

The NR_151716.1(LINC01807):​n.144+45047A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,768 control chromosomes in the GnomAD database, including 33,671 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 0.65 (33671 hom., cov: 30)
• Consequence: LINC01807 NR_151716.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

LINC01807 (HGNC:52610): (long intergenic non-protein coding RNA 1807)

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 (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01807	NR_151716.1	n.144+45047A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01807	ENST00000665053.1	n.126-77412A>G		intron_variant, non_coding_transcript_variant
LINC01807	ENST00000432481.2	n.144+45047A>G		intron_variant, non_coding_transcript_variant		3
LINC01807	ENST00000656071.1	n.313+2049A>G		intron_variant, non_coding_transcript_variant
LINC01807	ENST00000667233.1	n.366-77412A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98129 AN: 151650 Hom.: 33655 Cov.: 30

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.696

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.647 AC: 98165 AN: 151768 Hom.: 33671 Cov.: 30 AF XY: 0.655 AC XY: 48556 AN XY: 74176

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.700

Alfa AF: 0.707 Hom.: 19125

Bravo AF: 0.639

Asia WGS AF: 0.848 AC: 2953 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	0.10
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1435850; hg19: chr2-229430921;