chr16-20246545-C-T

Variant names:

• chr16-20246545-C-T
• rs12597579
• ENST00000804517.1:n.83+8950G>A

Variant summary

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

The ENST00000804517.1(ENSG00000304556):​n.83+8950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 152,156 control chromosomes in the GnomAD database, including 530 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 0.073 (530 hom., cov: 32)
• Consequence: ENSG00000304556 ENST00000804517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 42 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 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
ENSG00000304556	ENST00000804517.1	n.83+8950G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0729 AC: 11083 AN: 152038 Hom.: 528 Cov.: 32

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0882

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0730 AC: 11104 AN: 152156 Hom.: 530 Cov.: 32 AF XY: 0.0762 AC XY: 5667 AN XY: 74382

African (AFR) AF: 0.0945 AC: 3921 AN: 41510

American (AMR) AF: 0.0568 AC: 869 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0882 AC: 306 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1150 AN: 5178

South Asian (SAS) AF: 0.101 AC: 485 AN: 4810

European-Finnish (FIN) AF: 0.0770 AC: 815 AN: 10588

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0500 AC: 3398 AN: 68000

Other (OTH) AF: 0.0609 AC: 128 AN: 2102

Alfa AF: 0.0589 Hom.: 900

Bravo AF: 0.0757

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs12597579; hg19: chr16-20257867;