16-52073899-T-A

Position:

• chr16-52073899-T-A

Variant summary

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

The ENST00000622950.3(LINC02911):​n.4A>T 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 0.0193 in 459,272 control chromosomes in the GnomAD database, including 133 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 0.017 (35 hom., cov: 33)
  • Exomes 𝑓: 0.020 (98 hom.)
• Consequence: LINC02911 ENST00000622950.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49

Genes affected

LINC02911 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02911	XR_004837540.2	n.299A>T		non_coding_transcript_exon_variant	3/8
LINC02911	XR_007065208.1	n.299A>T		non_coding_transcript_exon_variant	3/8
LINC02911	XR_007065209.1	n.299A>T		non_coding_transcript_exon_variant	3/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02911	ENST00000622950.3	n.4A>T		non_coding_transcript_exon_variant	1/6	2
LINC02911	ENST00000566628.2	n.59+994A>T		intron_variant		3
LINC02911	ENST00000568524.5	n.197+994A>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0173 AC: 2626 AN: 152142 Hom.: 35 Cov.: 33

Gnomad AFR AF: 0.00425

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0256

Gnomad OTH AF: 0.0263

GnomAD3 exomes AF: 0.0192 AC: 2449 AN: 127442 Hom.: 35 AF XY: 0.0193 AC XY: 1345 AN XY: 69790

Gnomad AFR exome AF: 0.00214

Gnomad AMR exome AF: 0.0224

Gnomad ASJ exome AF: 0.0264

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0111

Gnomad FIN exome AF: 0.00433

Gnomad NFE exome AF: 0.0269

Gnomad OTH exome AF: 0.0366

GnomAD4 exome AF: 0.0203 AC: 6239 AN: 307012 Hom.: 98 Cov.: 1 AF XY: 0.0202 AC XY: 3532 AN XY: 174584

Gnomad4 AFR exome AF: 0.00564

Gnomad4 AMR exome AF: 0.0226

Gnomad4 ASJ exome AF: 0.0261

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0110

Gnomad4 FIN exome AF: 0.00486

Gnomad4 NFE exome AF: 0.0246

Gnomad4 OTH exome AF: 0.0273

GnomAD4 genome AF: 0.0172 AC: 2622 AN: 152260 Hom.: 35 Cov.: 33 AF XY: 0.0162 AC XY: 1209 AN XY: 74446

Gnomad4 AFR AF: 0.00424

Gnomad4 AMR AF: 0.0243

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.00443

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.0213 Hom.: 5

Bravo AF: 0.0185

Asia WGS AF: 0.00491 AC: 17 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0060
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17201113; hg19: chr16-52107811;