rs17058916

Variant names:

• chr18-76110782-G-A
• rs17058916
• ENST00000848884.1:n.227-14144C>T

Variant summary

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

The ENST00000848884.1(ENSG00000310300):​n.227-14144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 152,122 control chromosomes in the GnomAD database, including 288 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 0.039 (288 hom., cov: 32)
• Consequence: ENSG00000310300 ENST00000848884.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.48
• Publications: 0 publications found

Genes affected

ENSG00000310300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848884.1. 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
	ENSG00000310300	ENST00000848884.1		n.227-14144C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0394 AC: 5983 AN: 152004 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0393 AC: 5983 AN: 152122 Hom.: 288 Cov.: 32 AF XY: 0.0445 AC XY: 3310 AN XY: 74356

African (AFR) AF: 0.0180 AC: 749 AN: 41500

American (AMR) AF: 0.116 AC: 1768 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0721 AC: 250 AN: 3466

East Asian (EAS) AF: 0.190 AC: 984 AN: 5166

South Asian (SAS) AF: 0.0777 AC: 374 AN: 4814

European-Finnish (FIN) AF: 0.0505 AC: 534 AN: 10582

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

European-Non Finnish (NFE) AF: 0.0177 AC: 1206 AN: 68014

Other (OTH) AF: 0.0436 AC: 92 AN: 2110

Alfa AF: 0.0261 Hom.: 19

Bravo AF: 0.0442

Asia WGS AF: 0.129 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.71
PhyloP100		-4.5

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: rs17058916;

hg19: chr18-73822737;