rs9650199

Variant names:

• chr8-60433638-C-T
• rs9650199
• ENST00000476425.3:n.456-28389G>A

Variant summary

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

The ENST00000476425.3(LINC01301):​n.456-28389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,900 control chromosomes in the GnomAD database, including 4,317 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 0.22 (4317 hom., cov: 32)
• Consequence: LINC01301 ENST00000476425.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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.456-28389G>A		intron_variant	Intron 3 of 3	3
LINC01301	ENST00000530725.6	n.315-48232G>A		intron_variant	Intron 2 of 9	4
LINC01301	ENST00000656656.2	n.360-28389G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33626 AN: 151782 Hom.: 4308 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0961

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.222 AC: 33654 AN: 151900 Hom.: 4317 Cov.: 32 AF XY: 0.219 AC XY: 16239 AN XY: 74244

African (AFR) AF: 0.353 AC: 14607 AN: 41366

American (AMR) AF: 0.162 AC: 2467 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3464

East Asian (EAS) AF: 0.0965 AC: 499 AN: 5170

South Asian (SAS) AF: 0.174 AC: 839 AN: 4816

European-Finnish (FIN) AF: 0.170 AC: 1792 AN: 10550

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12430 AN: 67960

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.209 Hom.: 471

Bravo AF: 0.226

Asia WGS AF: 0.131 AC: 456 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	0.95
DANN	Benign	0.54
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9650199; hg19: chr8-61346197;