chr16-18071186-A-C

Variant names:

• chr16-18071186-A-C
• rs9284326
• ENST00000563866.1:n.49-67738T>G

Variant summary

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

The ENST00000563866.1(ENSG00000260242):​n.49-67738T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,076 control chromosomes in the GnomAD database, including 14,322 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 0.43 (14322 hom., cov: 32)
• Consequence: ENSG00000260242 ENST00000563866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 4 publications found

Genes affected

ENSG00000260242 (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 (SAS) allele frequency at 95% confidence interval = 0.508 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
ENSG00000260242	ENST00000563866.1	n.49-67738T>G		intron_variant	Intron 1 of 1	3
ENSG00000259929	ENST00000567304.1	n.144+80266T>G		intron_variant	Intron 1 of 2	4
ENSG00000309061	ENST00000838173.1	n.85-44T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65538 AN: 151956 Hom.: 14312 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.431 AC: 65597 AN: 152076 Hom.: 14322 Cov.: 32 AF XY: 0.433 AC XY: 32194 AN XY: 74346

African (AFR) AF: 0.385 AC: 15966 AN: 41486

American (AMR) AF: 0.476 AC: 7270 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2315 AN: 5160

South Asian (SAS) AF: 0.525 AC: 2528 AN: 4812

European-Finnish (FIN) AF: 0.439 AC: 4645 AN: 10586

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29846 AN: 67980

Other (OTH) AF: 0.455 AC: 962 AN: 2114

Alfa AF: 0.435 Hom.: 45257

Bravo AF: 0.427

Asia WGS AF: 0.479 AC: 1666 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	0.011
DANN	Benign	0.41
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9284326; hg19: chr16-18165043;