chr8-60491406-T-C

Variant names:

• chr8-60491406-T-C
• rs948421
• ENST00000476425.3:n.334+17241A>G

Variant summary

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

The ENST00000476425.3(LINC01301):​n.334+17241A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,934 control chromosomes in the GnomAD database, including 26,094 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 0.55 (26094 hom., cov: 31)
• Consequence: LINC01301 ENST00000476425.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 5 publications found

Genes affected

LINC01301 (HGNC:50464): (long intergenic non-protein coding RNA 1301)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

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
LINC01301	ENST00000476425.3	n.334+17241A>G		intron_variant	Intron 2 of 3	3
LINC01301	ENST00000530725.6	n.314+17241A>G		intron_variant	Intron 2 of 9	4
LINC01301	ENST00000532232.2	n.372+17241A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82865 AN: 151820 Hom.: 26042 Cov.: 31

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.546 AC: 82981 AN: 151934 Hom.: 26094 Cov.: 31 AF XY: 0.549 AC XY: 40722 AN XY: 74238

African (AFR) AF: 0.875 AC: 36274 AN: 41434

American (AMR) AF: 0.448 AC: 6840 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1771 AN: 3466

East Asian (EAS) AF: 0.571 AC: 2945 AN: 5162

South Asian (SAS) AF: 0.626 AC: 3009 AN: 4804

European-Finnish (FIN) AF: 0.452 AC: 4763 AN: 10538

Middle Eastern (MID) AF: 0.638 AC: 185 AN: 290

European-Non Finnish (NFE) AF: 0.380 AC: 25836 AN: 67952

Other (OTH) AF: 0.537 AC: 1135 AN: 2112

Alfa AF: 0.492 Hom.: 3541

Bravo AF: 0.556

Asia WGS AF: 0.653 AC: 2274 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	2.3
DANN	Benign	0.49
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs948421; hg19: chr8-61403965;