rs16869652

Variant names:

• chr6-33883396-G-A
• rs16869652
• ENST00000603883.1:n.227G>A

Your query was ambiguous. Multiple possible variants found:

• 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: ENSG00000271362 ENST00000603883.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

ENSG00000271362 (HGNC:56921):

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271362	ENST00000603883.1	n.227G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01016	ENST00000525912.1	n.75+10183C>T		intron_variant	Intron 1 of 1	3
LINC01016	ENST00000656906.1	n.339+9300C>T		intron_variant	Intron 1 of 1
LINC01016	ENST00000661137.1	n.309+8921C>T		intron_variant	Intron 2 of 2

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;