chr5-67653542-C-T

Variant names:

• chr5-67653542-C-T
• rs4976108
• ENST00000503106.5:n.520+33253C>T

Variant summary

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

The ENST00000503106.5(LINC02997):​n.520+33253C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,840 control chromosomes in the GnomAD database, including 4,260 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 0.18 (4260 hom., cov: 32)
• Consequence: LINC02997 ENST00000503106.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503106.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02997	ENST00000503106.5	TSL:4	n.520+33253C>T		intron	N/A
	LINC02997	ENST00000514368.2	TSL:3	n.125+33627C>T		intron	N/A
	LINC02997	ENST00000668508.1		n.248+33627C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26758 AN: 151720 Hom.: 4251 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.177 AC: 26801 AN: 151840 Hom.: 4260 Cov.: 32 AF XY: 0.175 AC XY: 12964 AN XY: 74200

African (AFR) AF: 0.404 AC: 16742 AN: 41396

American (AMR) AF: 0.140 AC: 2130 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.419 AC: 2156 AN: 5150

South Asian (SAS) AF: 0.108 AC: 518 AN: 4818

European-Finnish (FIN) AF: 0.0836 AC: 882 AN: 10550

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3735 AN: 67904

Other (OTH) AF: 0.163 AC: 342 AN: 2098

Alfa AF: 0.0580 Hom.: 131

Bravo AF: 0.196

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.8
DANN	Benign	0.61
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs4976108; hg19: chr5-66949370;