rs4823246

Positions:

• chr22-44615881-G-A
• chr22-44615881-G-C

Variant summary

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

The NR_044991.1(LINC00229):​n.390+6406C>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 0.664 in 151,944 control chromosomes in the GnomAD database, including 33,657 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 0.66 (33657 hom., cov: 31)
• Consequence: LINC00229 NR_044991.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

LINC00229 (HGNC:13240): (long intergenic non-protein coding RNA 229)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00229	NR_044991.1	n.390+6406C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00229	ENST00000443783.1	n.390+6406C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100815 AN: 151826 Hom.: 33629 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.664 AC: 100894 AN: 151944 Hom.: 33657 Cov.: 31 AF XY: 0.666 AC XY: 49438 AN XY: 74242

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.644

Alfa AF: 0.664 Hom.: 49708

Bravo AF: 0.669

Asia WGS AF: 0.690 AC: 2401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4823246; hg19: chr22-45011761;