rs16894980

Variant names:

• chr8-121252537-C-T
• rs16894980
• ENST00000784704.1:n.101+3523C>T

Variant summary

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

The ENST00000784704.1(ENSG00000302156):​n.101+3523C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,218 control chromosomes in the GnomAD database, including 733 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 0.072 (733 hom., cov: 32)
• Consequence: ENSG00000302156 ENST00000784704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 1 publications found

Genes affected

ENSG00000302156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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
ENSG00000302156	ENST00000784704.1	n.101+3523C>T		intron_variant	Intron 1 of 4
ENSG00000302156	ENST00000784705.1	n.154+3523C>T		intron_variant	Intron 2 of 2
ENSG00000302156	ENST00000784706.1	n.204+3523C>T		intron_variant	Intron 3 of 3
ENSG00000302156	ENST00000784707.1	n.101+3523C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10950 AN: 152100 Hom.: 733 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0721 AC: 10972 AN: 152218 Hom.: 733 Cov.: 32 AF XY: 0.0741 AC XY: 5514 AN XY: 74428

African (AFR) AF: 0.169 AC: 7005 AN: 41502

American (AMR) AF: 0.0961 AC: 1471 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3472

East Asian (EAS) AF: 0.0832 AC: 431 AN: 5182

South Asian (SAS) AF: 0.105 AC: 508 AN: 4816

European-Finnish (FIN) AF: 0.0307 AC: 326 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 910 AN: 68018

Other (OTH) AF: 0.0657 AC: 139 AN: 2116

Alfa AF: 0.0335 Hom.: 427

Bravo AF: 0.0798

Asia WGS AF: 0.123 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.50
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs16894980; hg19: chr8-122264777;