rs2007397

Variant names:

• chr21-41144265-G-A
• rs2007397
• ENST00000435493.3:n.571-850C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-41144265-G-A
• chr21-41144265-G-C

Variant summary

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

The ENST00000435493.3(LINC00323):​n.571-850C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,128 control chromosomes in the GnomAD database, including 8,128 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 0.32 (8128 hom., cov: 33)
• Consequence: LINC00323 ENST00000435493.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 12 publications found

Genes affected

LINC00323 (HGNC:19720): (long intergenic non-protein coding RNA 323)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00323	NR_024100.1	n.104-850C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00323	ENST00000435493.3	n.571-850C>T		intron_variant	Intron 3 of 3	3
LINC00323	ENST00000441268.2	n.173-850C>T		intron_variant	Intron 1 of 1	2
LINC00323	ENST00000446910.2	n.514+812C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47962 AN: 152010 Hom.: 8121 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.316 AC: 47997 AN: 152128 Hom.: 8128 Cov.: 33 AF XY: 0.320 AC XY: 23784 AN XY: 74366

African (AFR) AF: 0.214 AC: 8872 AN: 41500

American (AMR) AF: 0.463 AC: 7078 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3470

East Asian (EAS) AF: 0.367 AC: 1898 AN: 5170

South Asian (SAS) AF: 0.240 AC: 1159 AN: 4824

European-Finnish (FIN) AF: 0.375 AC: 3958 AN: 10568

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23125 AN: 67984

Other (OTH) AF: 0.334 AC: 704 AN: 2110

Alfa AF: 0.330 Hom.: 27804

Bravo AF: 0.322

Asia WGS AF: 0.307 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.0
DANN	Benign	0.40
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2007397; hg19: chr21-42516192;