10-33584433-T-C

Variant names:

• chr10-33584433-T-C
• rs1902408
• ENST00000457848.1:n.424-5064A>G

Variant summary

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

The ENST00000457848.1(LINC02628):​n.424-5064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,130 control chromosomes in the GnomAD database, including 51,389 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 0.82 (51389 hom., cov: 31)
• Consequence: LINC02628 ENST00000457848.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 publications found

Genes affected

LINC02628 (HGNC:54107): (long intergenic non-protein coding RNA 2628)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02628	NR_187516.1	n.289-5064A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02628	ENST00000457848.1	n.424-5064A>G		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124385 AN: 152012 Hom.: 51367 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.818 AC: 124458 AN: 152130 Hom.: 51389 Cov.: 31 AF XY: 0.817 AC XY: 60787 AN XY: 74374

African (AFR) AF: 0.715 AC: 29641 AN: 41480

American (AMR) AF: 0.856 AC: 13089 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.902 AC: 3130 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3431 AN: 5156

South Asian (SAS) AF: 0.754 AC: 3636 AN: 4820

European-Finnish (FIN) AF: 0.865 AC: 9153 AN: 10586

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59520 AN: 68012

Other (OTH) AF: 0.849 AC: 1792 AN: 2110

Alfa AF: 0.837 Hom.: 9016

Bravo AF: 0.817

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.42
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1902408; hg19: chr10-33873361;