4-116012923-C-T

Variant names:

• chr4-116012923-C-T
• rs7676999
• ENST00000508414.5:n.337-90788G>A

Variant summary

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

The ENST00000508414.5(ENSG00000293005):​n.337-90788G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,830 control chromosomes in the GnomAD database, including 2,475 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 (2475 hom., cov: 32)
• Consequence: ENSG00000293005 ENST00000508414.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 5 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=-0.85).
• 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.337-90788G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24705 AN: 151710 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.287

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: 0.163 AC: 24711 AN: 151830 Hom.: 2475 Cov.: 32 AF XY: 0.162 AC XY: 12035 AN XY: 74162

African (AFR) AF: 0.0551 AC: 2287 AN: 41474

American (AMR) AF: 0.147 AC: 2246 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3462

East Asian (EAS) AF: 0.141 AC: 729 AN: 5160

South Asian (SAS) AF: 0.262 AC: 1258 AN: 4808

European-Finnish (FIN) AF: 0.157 AC: 1647 AN: 10482

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14655 AN: 67900

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.175 Hom.: 3149

Bravo AF: 0.152

Asia WGS AF: 0.179 AC: 620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.56
DANN	Benign	0.70
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs7676999; hg19: chr4-116934079;