6-29510044-G-T

Position:

• chr6-29510044-G-T

Variant summary

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

The NR_183359.1(LINC02829):​n.623-224G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,172 control chromosomes in the GnomAD database, including 5,625 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 0.24 (5625 hom., cov: 33)
• Consequence: LINC02829 NR_183359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

LINC02829 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02829	NR_183359.1	n.623-224G>T		intron_variant
LINC02829	NR_183360.1	n.691-224G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02829	ENST00000436804.2	n.623-224G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36722 AN: 152054 Hom.: 5596 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.242 AC: 36786 AN: 152172 Hom.: 5625 Cov.: 33 AF XY: 0.234 AC XY: 17418 AN XY: 74410

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0998

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.224

Alfa AF: 0.176 Hom.: 3848

Bravo AF: 0.256

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.38
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1233478; hg19: chr6-29477821;