6-24730265-C-T

Variant names:

• chr6-24730265-C-T
• rs2067573
• ENST00000665572.2:n.267+8341C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000665572.2(LINC02828):​n.267+8341C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,192 control chromosomes in the GnomAD database, including 110 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 0.035 (110 hom., cov: 33)
• Consequence: LINC02828 ENST00000665572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 0 publications found

Genes affected

LINC02828 (HGNC:54359): (long intergenic non-protein coding RNA 2828)

ENSG00000307310 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0346 (5268/152192) while in subpopulation NFE AF = 0.0411 (2796/68012). AF 95% confidence interval is 0.0398. There are 110 homozygotes in GnomAd4. There are 2604 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 110 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02828	ENST00000665572.2	n.267+8341C>T		intron_variant	Intron 1 of 2
LINC02828	ENST00000668439.1	n.237+8341C>T		intron_variant	Intron 1 of 1
ENSG00000307310	ENST00000825031.1	n.623-3081G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5248 AN: 152074 Hom.: 109 Cov.: 33

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0501

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0346 AC: 5268 AN: 152192 Hom.: 110 Cov.: 33 AF XY: 0.0350 AC XY: 2604 AN XY: 74404

African (AFR) AF: 0.0280 AC: 1161 AN: 41526

American (AMR) AF: 0.0301 AC: 461 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0282 AC: 98 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4824

European-Finnish (FIN) AF: 0.0501 AC: 529 AN: 10564

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2796 AN: 68012

Other (OTH) AF: 0.0394 AC: 83 AN: 2108

Alfa AF: 0.0305 Hom.: 41

Bravo AF: 0.0325

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.48
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2067573; hg19: chr6-24730493;