rs13338289

Positions:

• chr16-58844717-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657379.1(ENSG00000245768):​n.650+88539G>A variant causes a intron, non coding transcript 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: ENST00000657379.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984867	XR_001752227.2	n.648-17318G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657379.1	n.650+88539G>A		intron_variant, non_coding_transcript_variant
	ENST00000500117.1	n.679+88539G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000565722.1	n.438-17318G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000568134.6	n.439-17318G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0639

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.236

Alfa AF: 0.147 Hom.: 1079

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13338289; hg19: chr16-58878621;