rs2007397

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024100.1(LINC00323):​n.104-850C>T variant causes a intron, non coding transcript 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 NR_024100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00323	NR_024100.1	n.104-850C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00323	ENST00000654244.1	n.238-850C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.334

Alfa AF: 0.333 Hom.: 17923

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2007397; hg19: chr21-42516192;