rs4794243

Positions:

• chr17-51371771-T-C
• chr17-51371771-T-G

Variant summary

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

The ENST00000663733.1(LINC02073):​n.1435+30460T>C 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 0.47 in 151,600 control chromosomes in the GnomAD database, including 18,040 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 0.47 (18040 hom., cov: 30)
• Consequence: LINC02073 ENST00000663733.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

LINC02073 (HGNC:52919): (long intergenic non-protein coding RNA 2073)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02073	ENST00000663733.1	n.1435+30460T>C		intron_variant, non_coding_transcript_variant
LINC02073	ENST00000650413.1	n.1735+30088T>C		intron_variant, non_coding_transcript_variant
LINC02073	ENST00000654524.1	n.1771+30088T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71191 AN: 151480 Hom.: 18007 Cov.: 30

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.470 AC: 71293 AN: 151600 Hom.: 18040 Cov.: 30 AF XY: 0.467 AC XY: 34604 AN XY: 74056

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.483

Alfa AF: 0.404 Hom.: 12716

Bravo AF: 0.493

Asia WGS AF: 0.596 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.52
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: rs4794243; hg19: chr17-49449132;