16-3269193-C-T

Position:

• chr16-3269193-C-T

Variant summary

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

The ENST00000703449.1(ENSG00000290183):​c.-171+5310C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,008 control chromosomes in the GnomAD database, including 22,552 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 0.53 (22552 hom., cov: 32)
• Consequence: ENST00000703449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

(HGNC:):

LINC00921 (HGNC:26830): (long intergenic non-protein coding RNA 921)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 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
	ENST00000703449.1	c.-171+5310C>T		intron_variant				ENSP00000515300	P1
LINC00921	ENST00000706009.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80257 AN: 151890 Hom.: 22506 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.529 AC: 80362 AN: 152008 Hom.: 22552 Cov.: 32 AF XY: 0.523 AC XY: 38872 AN XY: 74282

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.500

Alfa AF: 0.491 Hom.: 4834

Bravo AF: 0.545

Asia WGS AF: 0.374 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.85
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224243; hg19: chr16-3319193;