chr8-60373952-A-T

Variant names:

• chr8-60373952-A-T
• rs6471871
• ENST00000530725.6:n.592+10636T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000530725.6(LINC01301):​n.592+10636T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,220 control chromosomes in the GnomAD database, including 3,197 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 0.12 (3197 hom., cov: 32)
• Consequence: LINC01301 ENST00000530725.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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	ENST00000530725.6	n.592+10636T>A		intron_variant	Intron 4 of 9	4
LINC01301	ENST00000664011.1	n.415+10636T>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17900 AN: 152102 Hom.: 3186 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00217

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.118 AC: 17947 AN: 152220 Hom.: 3197 Cov.: 32 AF XY: 0.114 AC XY: 8459 AN XY: 74446

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.00217

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0704 Hom.: 268

Bravo AF: 0.134

Asia WGS AF: 0.0310 AC: 109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6471871; hg19: chr8-61286511;