rs13338289

Variant names:

• chr16-58844717-G-A
• rs13338289
• ENST00000500117.1:n.679+88539G>A

Variant summary

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

The ENST00000500117.1(ENSG00000245768):​n.679+88539G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,094 control chromosomes in the GnomAD database, including 5,187 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 0.22 (5187 hom., cov: 32)
• Consequence: ENSG00000245768 ENST00000500117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722
• Publications: 1 publications found

Genes affected

ENSG00000245768 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500117.1. 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
	ENSG00000245768	ENST00000500117.1	TSL:2	n.679+88539G>A		intron	N/A
	ENSG00000245768	ENST00000565722.1	TSL:2	n.438-17318G>A		intron	N/A
	ENSG00000245768	ENST00000568134.6	TSL:4	n.439-17318G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32854 AN: 151976 Hom.: 5158 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0639

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.216 AC: 32924 AN: 152094 Hom.: 5187 Cov.: 32 AF XY: 0.210 AC XY: 15642 AN XY: 74360

African (AFR) AF: 0.439 AC: 18202 AN: 41442

American (AMR) AF: 0.178 AC: 2714 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3464

East Asian (EAS) AF: 0.0728 AC: 377 AN: 5182

South Asian (SAS) AF: 0.115 AC: 554 AN: 4816

European-Finnish (FIN) AF: 0.0639 AC: 677 AN: 10598

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 9002 AN: 67992

Other (OTH) AF: 0.236 AC: 498 AN: 2112

Alfa AF: 0.155 Hom.: 1692

Bravo AF: 0.234

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13338289;

hg19: chr16-58878621;