4-116003028-T-C

Variant names:

• chr4-116003028-T-C
• rs17586843
• ENST00000508414.5:n.337-80893A>G

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.337-80893A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,998 control chromosomes in the GnomAD database, including 2,445 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 0.16 (2445 hom., cov: 32)
• Consequence: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 6 publications found

Genes affected

ENSG00000293005 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508414.5. 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
	ENSG00000293005	ENST00000508414.5	TSL:3	n.337-80893A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24312 AN: 151880 Hom.: 2444 Cov.: 32

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.160 AC: 24316 AN: 151998 Hom.: 2445 Cov.: 32 AF XY: 0.160 AC XY: 11852 AN XY: 74280

African (AFR) AF: 0.0456 AC: 1892 AN: 41506

American (AMR) AF: 0.145 AC: 2216 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1215 AN: 3464

East Asian (EAS) AF: 0.141 AC: 727 AN: 5146

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4814

European-Finnish (FIN) AF: 0.157 AC: 1652 AN: 10524

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14684 AN: 67972

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.152 Hom.: 1269

Bravo AF: 0.149

Asia WGS AF: 0.180 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.42
PhyloP100		-0.18

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: rs17586843;

hg19: chr4-116924184;