rs8017161

Positions:

• chr14-103096858-G-A

Variant summary

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

The NM_001077594.2(EXOC3L4):​c.-17+2018G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,062 control chromosomes in the GnomAD database, including 11,620 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 0.38 (11620 hom., cov: 32)
• Consequence: EXOC3L4 NM_001077594.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EXOC3L4	NM_001077594.2	c.-17+2018G>A		intron_variant		ENST00000688303.1	NP_001071062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EXOC3L4	ENST00000688303.1	c.-17+2018G>A		intron_variant			NM_001077594.2	ENSP00000509130.1
EXOC3L4	ENST00000687959.1	c.-317-1760G>A		intron_variant				ENSP00000508483.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58173 AN: 151946 Hom.: 11601 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.383 AC: 58215 AN: 152062 Hom.: 11620 Cov.: 32 AF XY: 0.386 AC XY: 28694 AN XY: 74340

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.406

Alfa AF: 0.401 Hom.: 21035

Bravo AF: 0.390

Asia WGS AF: 0.489 AC: 1700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8017161; hg19: chr14-103563195;