chr5-67472725-C-T

Variant names:

• chr5-67472725-C-T
• rs1387630
• ENST00000503106.5:n.251+93097C>T

Variant summary

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

The ENST00000503106.5(LINC02997):​n.251+93097C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 151,964 control chromosomes in the GnomAD database, including 60,935 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 0.90 (60935 hom., cov: 29)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934
• Publications: 3 publications found

Genes affected

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

ENSG00000250978 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928819	XR_241808.5	n.63+2690G>A		intron_variant	Intron 1 of 3
LOC101928819	XR_948390.3	n.85-4672G>A		intron_variant	Intron 1 of 3
LOC101928819	XR_948391.3	n.183-4672G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02997	ENST00000503106.5	n.251+93097C>T		intron_variant	Intron 1 of 3	4
ENSG00000250978	ENST00000508512.5	n.63+2690G>A		intron_variant	Intron 1 of 4	3
ENSG00000250978	ENST00000515184.2	n.379+2690G>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.895 AC: 135907 AN: 151846 Hom.: 60878 Cov.: 29

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.895 AC: 136021 AN: 151964 Hom.: 60935 Cov.: 29 AF XY: 0.899 AC XY: 66784 AN XY: 74262

African (AFR) AF: 0.909 AC: 37694 AN: 41460

American (AMR) AF: 0.922 AC: 14025 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3122 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5164 AN: 5172

South Asian (SAS) AF: 0.928 AC: 4464 AN: 4812

European-Finnish (FIN) AF: 0.910 AC: 9612 AN: 10568

Middle Eastern (MID) AF: 0.904 AC: 264 AN: 292

European-Non Finnish (NFE) AF: 0.869 AC: 59036 AN: 67952

Other (OTH) AF: 0.900 AC: 1900 AN: 2112

Alfa AF: 0.879 Hom.: 93684

Bravo AF: 0.898

Asia WGS AF: 0.961 AC: 3339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.26
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1387630; hg19: chr5-66768553;