14-103106478-A-G

Variant names:

• chr14-103106478-A-G
• rs944002
• NM_001077594.2:c.1467-307A>G

Variant summary

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

The NM_001077594.2(EXOC3L4):​c.1467-307A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,056 control chromosomes in the GnomAD database, including 4,822 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 0.25 (4822 hom., cov: 33)
• Consequence: EXOC3L4 NM_001077594.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 30 publications found

Genes affected

EXOC3L4 (HGNC:20120): (exocyst complex component 3 like 4) Predicted to enable SNARE binding activity. Predicted to be involved in exocyst localization and exocytosis. Predicted to be part of exocyst. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001077594.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOC3L4	NM_001077594.2	MANE Select	c.1467-307A>G		intron	N/A	NP_001071062.1
	EXOC3L4	NM_001394941.1		c.1467-307A>G		intron	N/A	NP_001381870.1
	EXOC3L4	NM_001394942.1		c.1467-307A>G		intron	N/A	NP_001381871.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXOC3L4	ENST00000688303.1	MANE Select	c.1467-307A>G		intron	N/A	ENSP00000509130.1
	EXOC3L4	ENST00000380069.7	TSL:1	c.1467-307A>G		intron	N/A	ENSP00000369409.3
	EXOC3L4	ENST00000687959.1		c.1467-307A>G		intron	N/A	ENSP00000508483.1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37538 AN: 151936 Hom.: 4811 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.247 AC: 37588 AN: 152056 Hom.: 4822 Cov.: 33 AF XY: 0.245 AC XY: 18190 AN XY: 74318

African (AFR) AF: 0.271 AC: 11221 AN: 41456

American (AMR) AF: 0.207 AC: 3161 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 866 AN: 3472

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5164

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2335 AN: 10580

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16452 AN: 67956

Other (OTH) AF: 0.266 AC: 561 AN: 2108

Alfa AF: 0.244 Hom.: 17040

Bravo AF: 0.249

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.82
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs944002; hg19: chr14-103572815;