16-72080103-C-T

Variant names:

• chr16-72080103-C-T
• rs217181
• ENST00000562153.6:n.284+8884G>A

Variant summary

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

The ENST00000562153.6(ENSG00000310525):​n.284+8884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,500 control chromosomes in the GnomAD database, including 3,310 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 0.20 (3310 hom., cov: 32)
• Consequence: ENSG00000310525 ENST00000562153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 47 publications found

Genes affected

ENSG00000310525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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
ENSG00000310525	ENST00000562153.6	n.284+8884G>A		intron_variant	Intron 3 of 5	4		ENSP00000454635.2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30644 AN: 151428 Hom.: 3304 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.202 AC: 30666 AN: 151500 Hom.: 3310 Cov.: 32 AF XY: 0.203 AC XY: 15002 AN XY: 73978

African (AFR) AF: 0.177 AC: 7328 AN: 41288

American (AMR) AF: 0.287 AC: 4372 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1571 AN: 5146

South Asian (SAS) AF: 0.126 AC: 603 AN: 4804

European-Finnish (FIN) AF: 0.209 AC: 2166 AN: 10346

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 290

European-Non Finnish (NFE) AF: 0.197 AC: 13408 AN: 67918

Other (OTH) AF: 0.192 AC: 404 AN: 2104

Alfa AF: 0.202 Hom.: 9790

Bravo AF: 0.212

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.5
DANN	Benign	0.87
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs217181; hg19: chr16-72114002;