ENST00000530725.6:n.805+3908G>A

Variant names:

• chr8-60318605-C-T
• rs10504308
• ENST00000530725.6:n.805+3908G>A

Variant summary

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

The ENST00000530725.6(LINC01301):​n.805+3908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 152,130 control chromosomes in the GnomAD database, including 801 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 0.086 (801 hom., cov: 32)
• Consequence: LINC01301 ENST00000530725.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 3 publications found

Genes affected

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

LOC105375864 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375864	XR_001745925.1	n.1042+3908G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01301	ENST00000530725.6	n.805+3908G>A		intron_variant	Intron 6 of 9	4
LINC01301	ENST00000819670.1	n.294+3908G>A		intron_variant	Intron 3 of 3
LINC01301	ENST00000819671.1	n.663+3908G>A		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13071 AN: 152012 Hom.: 798 Cov.: 32

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0860 AC: 13082 AN: 152130 Hom.: 801 Cov.: 32 AF XY: 0.0909 AC XY: 6757 AN XY: 74344

African (AFR) AF: 0.0217 AC: 902 AN: 41514

American (AMR) AF: 0.112 AC: 1718 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1047 AN: 5170

South Asian (SAS) AF: 0.191 AC: 918 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1510 AN: 10548

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0952 AC: 6471 AN: 68004

Other (OTH) AF: 0.0904 AC: 191 AN: 2112

Alfa AF: 0.0965 Hom.: 395

Bravo AF: 0.0794

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.50
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs10504308; hg19: chr8-61231164; COSMIC: COSV107189080;