16-80897313-G-T

Variant names:

• chr16-80897313-G-T
• rs889519
• ENST00000650780.1:c.82-66556C>A

Variant summary

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

The ENST00000650780.1(ENSG00000286221):​c.82-66556C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,142 control chromosomes in the GnomAD database, including 2,259 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 0.12 (2259 hom., cov: 33)
• Consequence: ENSG00000286221 ENST00000650780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000286221 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 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
ENSG00000286221	ENST00000650780.1	c.82-66556C>A		intron_variant	Intron 2 of 2			ENSP00000498782.1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18549 AN: 152024 Hom.: 2256 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.0784

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.122 AC: 18581 AN: 152142 Hom.: 2259 Cov.: 33 AF XY: 0.122 AC XY: 9067 AN XY: 74390

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.0781

Gnomad4 FIN AF: 0.0610

Gnomad4 NFE AF: 0.0386

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0654 Hom.: 208

Bravo AF: 0.131

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs889519; hg19: chr16-80931210;