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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984867	XR_001752227.2	n.648-17318G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000245768	ENST00000500117.1	n.679+88539G>A		intron_variant	Intron 2 of 3	2
ENSG00000245768	ENST00000565722.1	n.438-17318G>A		intron_variant	Intron 1 of 1	2
ENSG00000245768	ENST00000568134.6	n.439-17318G>A		intron_variant	Intron 3 of 3	4

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 v4.3

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

Other links and lift over

dbSNP: rs13338289; hg19: chr16-58878621;