rs6471871

Positions:

• chr8-60373952-A-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01301	ENST00000530725.6	n.592+10636T>A		intron_variant, non_coding_transcript_variant		4
LINC01301	ENST00000664011.1	n.415+10636T>A		intron_variant, non_coding_transcript_variant

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;