rs4794243

Variant names:

• chr17-51371771-T-C
• rs4794243
• ENST00000650413.1:n.1735+30088T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000650413.1(LINC02073):​n.1735+30088T>C variant causes a intron 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 ENST00000650413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02073	ENST00000650413.1	n.1735+30088T>C		intron_variant	Intron 3 of 4
LINC02073	ENST00000654524.2	n.1771+30088T>C		intron_variant	Intron 3 of 4
LINC02073	ENST00000663733.2	n.1456+30460T>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.646 AC: 26651 AN: 41274

American (AMR) AF: 0.471 AC: 7183 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1692 AN: 3472

East Asian (EAS) AF: 0.589 AC: 3016 AN: 5120

South Asian (SAS) AF: 0.534 AC: 2554 AN: 4786

European-Finnish (FIN) AF: 0.333 AC: 3506 AN: 10518

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25183 AN: 67868

Other (OTH) AF: 0.483 AC: 1016 AN: 2104

Alfa AF: 0.419 Hom.: 20252

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4794243; hg19: chr17-49449132;