6-84468550-T-C

Position:

• chr6-84468550-T-C

Variant summary

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

The ENST00000454172.5(LINC01611):​n.135-24099A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,840 control chromosomes in the GnomAD database, including 20,588 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 0.52 (20588 hom., cov: 31)
• Consequence: LINC01611 ENST00000454172.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439

Genes affected

LINC01611 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01611	NR_132100.1	n.217+2241A>G		intron_variant
LOC107986620	XR_001744235.2	n.191+15223T>C		intron_variant
LOC107986620	XR_001744236.1	n.134+15223T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01611	ENST00000428896.1	n.217+2241A>G		intron_variant		5
LINC01611	ENST00000454172.5	n.135-24099A>G		intron_variant		3
LINC01611	ENST00000454981.5	n.114+2241A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78672 AN: 151722 Hom.: 20555 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.519 AC: 78763 AN: 151840 Hom.: 20588 Cov.: 31 AF XY: 0.519 AC XY: 38522 AN XY: 74172

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.553

Alfa AF: 0.539 Hom.: 46076

Bravo AF: 0.520

Asia WGS AF: 0.623 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9362054; hg19: chr6-85178268;