rs1604797

Variant names:

• chr11-11111902-T-A
• rs1604797
• ENST00000647635.1:n.159-5934T>A

Variant summary

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

The ENST00000647635.1(LINC02752):​n.159-5934T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,946 control chromosomes in the GnomAD database, including 5,996 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 0.28 (5996 hom., cov: 32)
• Consequence: LINC02752 ENST00000647635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 1 publications found

Genes affected

LINC02752 (HGNC:54272): (long intergenic non-protein coding RNA 2752)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647635.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02752	ENST00000647635.1		n.159-5934T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41909 AN: 151828 Hom.: 5976 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.276 AC: 41975 AN: 151946 Hom.: 5996 Cov.: 32 AF XY: 0.271 AC XY: 20156 AN XY: 74304

African (AFR) AF: 0.349 AC: 14438 AN: 41406

American (AMR) AF: 0.274 AC: 4178 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3468

East Asian (EAS) AF: 0.191 AC: 987 AN: 5166

South Asian (SAS) AF: 0.202 AC: 973 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 1995 AN: 10550

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17611 AN: 67948

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.273 Hom.: 705

Bravo AF: 0.285

Asia WGS AF: 0.175 AC: 610 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.49
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1604797; hg19: chr11-11133449;