rs4823246

Variant names:

• chr22-44615881-G-A
• rs4823246
• ENST00000443783.2:n.402+6406C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000443783.2(LINC00229):​n.402+6406C>T variant causes a intron 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 ENST00000443783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00229	NR_044991.1	n.390+6406C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00229	ENST00000443783.2	n.402+6406C>T		intron_variant	Intron 3 of 4	2
LINC00229	ENST00000834593.1	n.271+6517C>T		intron_variant	Intron 3 of 4
LINC00229	ENST00000834594.1	n.382+6406C>T		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.644 AC: 26692 AN: 41442

American (AMR) AF: 0.731 AC: 11169 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1950 AN: 3464

East Asian (EAS) AF: 0.645 AC: 3315 AN: 5138

South Asian (SAS) AF: 0.734 AC: 3532 AN: 4814

European-Finnish (FIN) AF: 0.632 AC: 6677 AN: 10572

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45508 AN: 67926

Other (OTH) AF: 0.644 AC: 1359 AN: 2110

Alfa AF: 0.666 Hom.: 124506

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4823246; hg19: chr22-45011761;