rs7705123

Variant names:

• chr5-67684048-T-C
• rs7705123
• ENST00000503106.5:n.520+63759T>C

Variant summary

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

The ENST00000503106.5(LINC02997):​n.520+63759T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,998 control chromosomes in the GnomAD database, including 13,455 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 0.39 (13455 hom., cov: 32)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 2 publications found

Genes affected

LINC02997 (HGNC:56113): (long intergenic non-protein coding RNA 2997)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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
LINC02997	ENST00000503106.5	n.520+63759T>C		intron_variant	Intron 3 of 3	4
LINC02997	ENST00000514368.2	n.125+64133T>C		intron_variant	Intron 1 of 5	3
LINC02997	ENST00000668508.1	n.248+64133T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59642 AN: 151880 Hom.: 13424 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.393 AC: 59732 AN: 151998 Hom.: 13455 Cov.: 32 AF XY: 0.395 AC XY: 29317 AN XY: 74314

African (AFR) AF: 0.574 AC: 23772 AN: 41442

American (AMR) AF: 0.430 AC: 6560 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3748 AN: 5164

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4822

European-Finnish (FIN) AF: 0.332 AC: 3509 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18532 AN: 67960

Other (OTH) AF: 0.397 AC: 835 AN: 2104

Alfa AF: 0.330 Hom.: 1231

Bravo AF: 0.414

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.36
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7705123; hg19: chr5-66979876;