5-164297275-A-G

Variant names:

• chr5-164297275-A-G
• rs2964911
• ENST00000767702.1:n.632A>G

Variant summary

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

The ENST00000767702.1(LINC03000):​n.632A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,944 control chromosomes in the GnomAD database, including 3,308 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 0.20 (3308 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC03000 ENST00000767702.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 2 publications found

Genes affected

LINC03000 (HGNC:56116): (long intergenic non-protein coding RNA 3000)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767702.1. 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
	LINC03000	ENST00000767702.1		n.632A>G		non_coding_transcript_exon	Exon 1 of 1
	LINC03000	ENST00000517508.5	TSL:4	n.501+79A>G		intron	N/A
	LINC03000	ENST00000519329.3	TSL:3	n.848+79A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30968 AN: 151826 Hom.: 3305 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.204 AC: 30974 AN: 151944 Hom.: 3308 Cov.: 32 AF XY: 0.206 AC XY: 15271 AN XY: 74270

African (AFR) AF: 0.268 AC: 11108 AN: 41454

American (AMR) AF: 0.184 AC: 2807 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1548 AN: 5148

South Asian (SAS) AF: 0.126 AC: 607 AN: 4812

European-Finnish (FIN) AF: 0.188 AC: 1986 AN: 10552

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11777 AN: 67936

Other (OTH) AF: 0.186 AC: 392 AN: 2108

Alfa AF: 0.181 Hom.: 1525

Bravo AF: 0.211

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2964911; hg19: chr5-163724281;