16-80897313-G-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000286221 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650780.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286221	ENST00000650780.1		c.82-66556C>A		intron	N/A	ENSP00000498782.1
	ENSG00000286221	ENST00000650881.1		n.148-57091C>A		intron	N/A
	ENSG00000286221	ENST00000651567.1		n.82-57091C>A		intron	N/A	ENSP00000499144.1

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

African (AFR) AF: 0.321 AC: 13295 AN: 41446

American (AMR) AF: 0.0595 AC: 910 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3468

East Asian (EAS) AF: 0.0645 AC: 333 AN: 5162

South Asian (SAS) AF: 0.0781 AC: 377 AN: 4830

European-Finnish (FIN) AF: 0.0610 AC: 646 AN: 10588

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0386 AC: 2628 AN: 68028

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.51
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs889519; hg19: chr16-80931210;