ENST00000832588.1:n.335-1076T>C

Variant names:

• chr16-87815297-T-C
• rs9921866
• ENST00000832588.1:n.335-1076T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000832588.1(ENSG00000308222):​n.335-1076T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,112 control chromosomes in the GnomAD database, including 33,923 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 0.65 (33923 hom., cov: 33)
• Consequence: ENSG00000308222 ENST00000832588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 12 publications found

Genes affected

ENSG00000308222 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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
ENSG00000308222	ENST00000832588.1	n.335-1076T>C		intron_variant	Intron 2 of 2
ENSG00000308222	ENST00000832589.1	n.73-1076T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99497 AN: 151994 Hom.: 33881 Cov.: 33

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.655 AC: 99587 AN: 152112 Hom.: 33923 Cov.: 33 AF XY: 0.665 AC XY: 49424 AN XY: 74358

African (AFR) AF: 0.786 AC: 32621 AN: 41508

American (AMR) AF: 0.722 AC: 11033 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3468

East Asian (EAS) AF: 0.953 AC: 4926 AN: 5168

South Asian (SAS) AF: 0.804 AC: 3881 AN: 4828

European-Finnish (FIN) AF: 0.617 AC: 6518 AN: 10564

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 37000 AN: 67976

Other (OTH) AF: 0.616 AC: 1300 AN: 2112

Alfa AF: 0.577 Hom.: 104275

Bravo AF: 0.666

Asia WGS AF: 0.869 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.28
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs9921866; hg19: chr16-87848903;