rs2329946

Variant names:

• chr21-44995392-C-T
• rs2329946
• ENST00000569966.1:n.-207G>A

Variant summary

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

The ENST00000569966.1(LINC00165):​n.-207G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,286 control chromosomes in the GnomAD database, including 2,631 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 (2631 hom., cov: 34)
• Consequence: LINC00165 ENST00000569966.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 1 publications found

Genes affected

LINC00165 (HGNC:33166): (long intergenic non-protein coding RNA 165)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000569966.1. 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
	LINC00165	NR_170266.1		n.-190G>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00165	ENST00000569966.1	TSL:6	n.-207G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27324 AN: 152168 Hom.: 2632 Cov.: 34

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.179 AC: 27330 AN: 152286 Hom.: 2631 Cov.: 34 AF XY: 0.179 AC XY: 13347 AN XY: 74462

African (AFR) AF: 0.124 AC: 5166 AN: 41568

American (AMR) AF: 0.243 AC: 3713 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 831 AN: 3468

East Asian (EAS) AF: 0.176 AC: 909 AN: 5178

South Asian (SAS) AF: 0.117 AC: 566 AN: 4832

European-Finnish (FIN) AF: 0.170 AC: 1807 AN: 10618

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13743 AN: 68006

Other (OTH) AF: 0.177 AC: 374 AN: 2116

Alfa AF: 0.193 Hom.: 367

Bravo AF: 0.185

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.42
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs2329946; hg19: chr21-46415307;