rs1836803

Positions:

• chr4-112083235-T-A
• chr4-112083235-T-G

Variant summary

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

The ENST00000679735.1(LINC02945):​n.85+28954A>T 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 0.352 in 152,052 control chromosomes in the GnomAD database, including 10,006 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 0.35 (10006 hom., cov: 32)
• Consequence: LINC02945 ENST00000679735.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

Genes affected

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02945	ENST00000679735.1	n.85+28954A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53413 AN: 151934 Hom.: 9998 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.352 AC: 53468 AN: 152052 Hom.: 10006 Cov.: 32 AF XY: 0.352 AC XY: 26183 AN XY: 74300

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.349

Alfa AF: 0.321 Hom.: 1024

Bravo AF: 0.367

Asia WGS AF: 0.402 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1836803; hg19: chr4-113004391;