16-20250080-T-C

Variant names:

• chr16-20250080-T-C
• rs7203219
• ENST00000804517.1:n.83+5415A>G

Variant summary

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

The ENST00000804517.1(ENSG00000304556):​n.83+5415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,146 control chromosomes in the GnomAD database, including 5,781 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 0.24 (5781 hom., cov: 32)
• Consequence: ENSG00000304556 ENST00000804517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 4 publications found

Genes affected

ENSG00000304556 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804517.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304556	ENST00000804517.1		n.83+5415A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35730 AN: 152028 Hom.: 5749 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.235 AC: 35821 AN: 152146 Hom.: 5781 Cov.: 32 AF XY: 0.236 AC XY: 17557 AN XY: 74376

African (AFR) AF: 0.459 AC: 19039 AN: 41472

American (AMR) AF: 0.187 AC: 2861 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3466

East Asian (EAS) AF: 0.244 AC: 1259 AN: 5170

South Asian (SAS) AF: 0.115 AC: 556 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2297 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8761 AN: 68012

Other (OTH) AF: 0.178 AC: 377 AN: 2116

Alfa AF: 0.130 Hom.: 866

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs7203219; hg19: chr16-20261402;