rs16880395

Variant names:

• chr4-28238041-C-T
• rs16880395
• ENST00000668598.1:n.92+11981C>T

Variant summary

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

The ENST00000668598.1(ENSG00000286321):​n.92+11981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,818 control chromosomes in the GnomAD database, including 4,097 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 0.23 (4097 hom., cov: 32)
• Consequence: ENSG00000286321 ENST00000668598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 3 publications found

Genes affected

ENSG00000286321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374557	NR_188396.1	n.287+22893C>T		intron_variant	Intron 2 of 4
LOC105374557	NR_188397.1	n.287+22893C>T		intron_variant	Intron 2 of 3
LOC105374557	NR_188398.1	n.287+22893C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286321	ENST00000668598.1	n.92+11981C>T		intron_variant	Intron 1 of 1
ENSG00000286321	ENST00000742923.1	n.222+22893C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34276 AN: 151700 Hom.: 4095 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.226 AC: 34299 AN: 151818 Hom.: 4097 Cov.: 32 AF XY: 0.220 AC XY: 16322 AN XY: 74202

African (AFR) AF: 0.292 AC: 12077 AN: 41400

American (AMR) AF: 0.177 AC: 2695 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 608 AN: 3460

East Asian (EAS) AF: 0.0686 AC: 354 AN: 5162

South Asian (SAS) AF: 0.105 AC: 506 AN: 4812

European-Finnish (FIN) AF: 0.171 AC: 1806 AN: 10564

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15513 AN: 67866

Other (OTH) AF: 0.216 AC: 456 AN: 2108

Alfa AF: 0.218 Hom.: 653

Bravo AF: 0.230

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs16880395; hg19: chr4-28239663;