rs16869652

Positions:

• chr6-33883396-G-A
• chr6-33883396-G-T

Variant summary

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

The ENST00000603883.1(ENSG00000271362):​n.227G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0896 in 523,776 control chromosomes in the GnomAD database, including 2,477 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 0.11 (1063 hom., cov: 32)
  • Exomes 𝑓: 0.081 (1414 hom.)
• Consequence: ENST00000603883.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

(HGNC:):

LINC01016 (HGNC:48991): (long intergenic non-protein coding RNA 1016)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000603883.1	n.227G>A		non_coding_transcript_exon_variant	1/1
LINC01016	ENST00000525912.1	n.75+10183C>T		intron_variant, non_coding_transcript_variant		3
LINC01016	ENST00000656906.1	n.339+9300C>T		intron_variant, non_coding_transcript_variant
LINC01016	ENST00000661137.1	n.309+8921C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16712 AN: 152048 Hom.: 1061 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0812 AC: 30191 AN: 371608 Hom.: 1414 Cov.: 0 AF XY: 0.0812 AC XY: 16705 AN XY: 205632

Gnomad4 AFR exome AF: 0.168

Gnomad4 AMR exome AF: 0.0684

Gnomad4 ASJ exome AF: 0.124

Gnomad4 EAS exome AF: 0.0434

Gnomad4 SAS exome AF: 0.0695

Gnomad4 FIN exome AF: 0.0641

Gnomad4 NFE exome AF: 0.0846

Gnomad4 OTH exome AF: 0.0813

GnomAD4 genome AF: 0.110 AC: 16724 AN: 152168 Hom.: 1063 Cov.: 32 AF XY: 0.107 AC XY: 7994 AN XY: 74390

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0935

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.0745

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0903 Hom.: 991

Bravo AF: 0.113

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16869652; hg19: chr6-33851173;